Virtual Journal of Biological Physics Research

Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistance

Megan H. Powdrill, Egor P. Tchesnokov, Robert A. Kozak, Rodney S. Russell, Ross Martin et al.
The development of resistance to direct-acting antivirals (DAAs) targeting the hepatitis C virus (HCV) can compromise therapy. However, mechanisms that determine prevalence and frequency of resistance-conferring mutations remain elusive. Here, we studied the fidelity of the HCV RNA-dependent RNA po ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20509 (2011)] published Thu Dec 22, 2011.

Solar hydrogen-producing bionanodevice outperforms natural photosynthesis

Carolyn E. Lubner, Amanda M. Applegate, Philipp Knorzer, Alexander Ganago, Donald A. Bryant et al.
Although a number of solar biohydrogen systems employing photosystem I (PSI) have been developed, few attain the electron transfer throughput of oxygenic photosynthesis. We have optimized a biological/organic nanoconstruct that directly tethers F, the terminal [4Fe-4S] cluster of PSI from Synechoco ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20988 (2011)] published Thu Dec 29, 2011.

Graphitic Tribological Layers in Metal-on-Metal Hip Replacements

Y. Liao, R. Pourzal, M. A. Wimmer, J. J. Jacobs, A. Fischer et al.
Arthritis is a leading cause of disability, and when nonoperative methods have failed, a prosthetic implant is a cost-effective and clinically successful treatment. Metal-on-metal replacements are an attractive implant technology, a lower-wear alternative to metal-on-polyethylene devices. Relatively ... [Science 334, 1687 (2011)] published Thu Dec 22, 2011.

Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements

Anton Barty, Carl Caleman, Andrew Aquila, Nicusor Timneanu, Lukas Lomb et al.
X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been pred ... [Nat. Photonics 6, 35 (2011)] published Thu Dec 22, 2011.

Transient two-dimensional spectroscopy with linear absorption corrections applied to temperature-jump two-dimensional infrared

Kevin C. Jones, Ziad Ganim, Chunte Sam Peng, and Andrei Tokmakoff
Multidimensional spectroscopies provide increased spectral information but time resolution is often limited by the picosecond lifetimes of the transitions they probe. At the expense of additional complexity, transient multidimensional techniques extend the accessible timescales for studying nonequil ... [J. Opt. Soc. Am. B 29, 118 (2011)] published Tue Dec 27, 2011.

Regio selective functionalisation of gold nanoparticles with DNA

Elaine Spain, Brianna Miner, Tia E. Keyes, and Robert J. Forster
Suspensions of electrocatalytic gold nanoparticles with radii as small as 83 13 nm that are functionalised with DNA only in one region have been created using templated electrodeposition. The integrity of the bound DNA following nanoparticle desorption from the electrode is demonstrated by detectin ... [Chem. Commun. 48, 838 (2011)] published Fri Dec 16, 2011.

Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine

Christopher L. Warren, Jianfei Zhao, Kimberly Glass, Vikas Rishi, Aseem Z. Ansari et al.
We synthesized customized double-stranded DNA microarrays including methyl-5-cytosine at CpG dinucleotides and produced all 163,555 possible 8-mers (un-, hemi-, and di-methylated) to gain insight into how methylation affects transcription factor binding. An antibody to methyl-5-cytidine showed great ... [Lab Chip 12, 376 (2011)] published Fri Dec 16, 2011.

All-silica nanofluidic devices for DNA-analysis fabricated by imprint of solgel silica with silicon stamp

Morten Bo Mikkelsen, Alban A. Letailleur, Elin Sondergard, Etienne Barthel, Jeremie Teisseire et al.
We present a simple and cheap method for fabrication of silica nanofluidic devices for single-molecule studies. By imprinting solgel materials with a multi-level stamp comprising micro- and nanofeatures, channels of different depth are produced in a single process step. Calcination of the imprinted ... [Lab Chip 12, 262 (2011)] published Fri Dec 16, 2011.

An integrated chip for immunofluorescence and its application to analyze lysosomal storage disorders

Jie Shen, Ying Zhou, Tu Lu, Junya Peng, Zhixiang Lin et al.
Immunofluorescence (IF) is a common method to observe protein distribution and localization at the single-cell level through wide-field fluorescence or confocal microscopy. Conventional protocol for IF staining of cells typically requires a large amount of reagents, especially antibodies, and notice ... [Lab Chip 12, 317 (2011)] published Fri Dec 16, 2011.

Time-resolved imaging refractometry of microbicidal films using quantitative phase microscopy

Matthew T. Rinehart, Tyler K. Drake, Francisco E. Robles, Lisa C. Rohan, David Katz et al.
Quantitative phase microscopy is applied to image temporal changes in the refractive index (RI) distributions of solutions created by microbicidal films undergoing hydration. We present a novel method of using an engineered polydimethylsiloxane structure as a static phase reference to facilitate cal ... [J. Biomed. Opt. 16, 120510 (2011)] published Mon Dec 19, 2011.

Lensless multispectral digital in-line holographic microscope

James P. Ryle, Susan McDonnell, and John T. Sheridan
An compact multispectral digital in-line holographic microscope (DIHM) is developed that emulates Gabor's original holographic principle. Using sources of varying spatial coherence (laser, LED), holographic images of objects, including optical fiber, latex microspheres, and cancer cells, are success ... [J. Biomed. Opt. 16, 126004 (2011)] published Fri Dec 16, 2011.

Solid-state sensor incorporated in microfluidic chip and magnetic-bead enzyme immobilization approach for creatinine and glucose detection in serum

Yen-Heng Lin, Chien-Hung Chiang, Min-Hsien Wu, Tung-Ming Pan, Ji-Dung Luo et al.
Solid-state sensors are stable and inexpensive electric transducers for biomedical measurement. This study proposes a microfluidic chip incorporated with a solid-state sensor for measuring glucose and creatinine in blood serum. Magnetic beads are employed to immobilize enzymes and deliver them in a ... [Appl. Phys. Lett. 99, 253704 (2011)] published Wed Dec 21, 2011.

Direct observation of dynamic force propagation between focal adhesions of cells on microposts by atomic force microscopy

Akinori Okada, Yusuke Mizutani, Agus Subagyo, Hirotaka Hosoi, Motonori Nakamura et al.
We investigated dynamic force propagation between focal adhesions of fibroblast cells cultured on polydimethylsiloxane micropost substrates, by atomic force microscopy. Live cells were mechanically modulated by the atomic force microscopy probe bound to cell apical surfaces at 0.010.5 Hz, while micr ... [Appl. Phys. Lett. 99, 263703 (2011)] published Thu Dec 29, 2011.

Flow-enhanced transient response in whispering gallery mode biosensors

Jason M. Gamba and Richard C. Flagan
Whispering gallery mode (WGM) optical resonator sensors are an extremely sensitive label-free technology for detecting the binding of biomolecules in solution. To better understand the fast transient response observed with these devices, we model mass transfer to spherical and toroidal WGM sensors o ... [Appl. Phys. Lett. 99, 253705 (2011)] published Wed Dec 21, 2011.

Analysis of hysteresis characteristics of silicon nanowire biosensors in aqueous environment

Hyeri Jang, Jieun Lee, Jung Han Lee, Sungmin Seo, Byung-Gook Park et al.
The hysteresis phenomenon has been widely observed in transfer characteristics of silicon nanowire (SiNW) biosensor devices in aqueous environment. Considering the experimental observation in the change of the liquid potential due to the charge flow through the oxide layer, we build up an electrical ... [Appl. Phys. Lett. 99, 252103 (2011)] published Tue Dec 20, 2011.

Molecular Gas Sensing Below Parts Per Trillion: Radiocarbon-Dioxide Optical Detection

I. Galli, S. Bartalini, S. Borri, P. Cancio, D. Mazzotti et al.
Radiocarbon (C) concentrations at a 43 parts-per-quadrillion level are measured by using saturated-absorption cavity ringdown spectroscopy by exciting radiocarbon-dioxide (CO) molecules at the 4.5 [mu]m wavelength. The ultimate sensitivity limits of molecular trace gas sensing are pushed down to at ... [Phys. Rev. Lett. 107, 270802 ] published .

Effects of cell cycle on the uptake of water soluble quantum dots by cells

Shen Zheng, Ji-Yao Chen, Jun-Yong Wang, Lu-Wei Zhou, and Qian Peng
Quantum dots (QDs) with excellent optical properties have become powerful candidates for cell imaging. Although numerous reports have studied the uptake of QDs by cells, little information exists on the effects of cell cycle on the cellular QD uptake. In this report, the effects of cell cycle on the ... [J. Appl. Phys. 110, 124701 (2011)] published Mon Dec 19, 2011.

Semiconductors for early detection and therapy

P. Georgiou and C. Toumazou
Presented is an overview of how semiconductor technology is now being used for early detection on therapy of disease. Specifically two areas are described, which are currently utilising CMOS technology with tremendous benefit in healthcare. The first is in genomics, whereby advances in CMOS-based IS ... [Electron. Lett. 47, S4 ] published .

Johns Hopkins on the chip: microsystems and cognitive machines for sustainable, affordable, personalised medicine and healthcare

A.G. Andreou
Semiconductor technology is contributing to the advancement of biotechnology, medicine and healthcare delivery in ways that it was never envisioned from chip micro-arrays, to scientific grade CMOS imagers and ion sensing arrays to implantable prosthesis. This exponential growth of sensory microsyst ... [Electron. Lett. 47, S34 ] published .

Self-aligned wet-cell for hydrated microbiology observation in TEM

Tsu-Wei Huang, Shih-Yi Liu, Yun-Ju Chuang, Hsin-Yi Hsieh, Chun-Ying Tsai et al.
This paper describes a Self-Aligned Wet (SAW) cell suitable for direct-cell or bacteria incubation and observation in a wet environment inside a transmission electron microscope. This SAW cell is fabricated by a bulk-micromachining process and composed of two structurally complementary counterparts ... [Lab Chip 12, 340 (2011)] published Fri Dec 16, 2011.

Microfluidic device to investigate factors affecting performance in biosensors designed for transdermal applications

Jakub Trzebinski, Sanjiv Sharma, Anna Radomska-Botelho Moniz, Kostis Michelakis, Yangyang Zhang et al.
In this work we demonstrate a novel microfluidic based platform to investigate the performance of 3D out-of-plane microspike array based glucose and lactate biosensors. The microspike array was bonded with a glass slide and modified with glucose oxidase or lactate oxidase using covalent coupling che ... [Lab Chip 12, 348 (2011)] published Fri Dec 16, 2011.

Imaging the cellular response to transient shear stress using stroboscopic digital holography

Maciej Antkowiak, Yoshihiko Arita, Kishan Dholakia, and Frank Gunn-Moore
We use stroboscopic quantitative phase microscopy to study cell deformation and the response to cavitation bubbles and transient shear stress resulting from laser-induced breakdown of an optically trapped nanoparticle. A bi-directional transient displacement of cytoplasm is observed during expansion ... [J. Biomed. Opt. 16, 120508 (2011)] published Fri Dec 16, 2011.

DNA hybridization detection in a miniaturized electromagnetic band gap resonator

Mircea Dragoman, Alina Cismaru, Antonio Radoi, Marius Voicu, and Daniela Dragoman
The hybridization of the deoxyribonucleic acid (DNA) is sensed in a miniaturized electromagnetic band gap resonator, which has a resonance frequency f=17.3 GHz when unloaded. The resonance frequency f is shifted to the left when a single-stranded DNA is immobilized on the resonator and to the right ... [Appl. Phys. Lett. 99, 253106 (2011)] published Wed Dec 21, 2011.

Extracellular voltage noise probes the interface between retina and silicon chip

Ralf Zeitler, Peter Fromherz, and Gunther Zeck
Neuroprosthetic devices rely on a tight contact between electrodes and neurons in the interfaced tissue. A simple method to probe the contact properties in a non-invasive way would be highly attractive. Here we show for retinal tissue that crucial electrical properties of the interface can be extrac ... [Appl. Phys. Lett. 99, 263702 (2011)] published Wed Dec 28, 2011.

Background-Free Nonlinear Microspectroscopy with Vibrational Molecular Interferometry

Erik T. Garbacik, Jeroen P. Korterik, Cees Otto, Shaul Mukamel, Jennifer L. Herek et al.
We demonstrate a method for performing nonlinear microspectroscopy that provides an intuitive and unified description of the various signal contributions, and allows the direct extraction of the vibrational response. Three optical fields create a pair of Stokes Raman pathways that interfere in the s ... [Phys. Rev. Lett. 107, 253902 ] published .

Growth propagation of yeast in linear arrays of microfluidic chambers over many generations

Li Wang, Jiaji Liu, Xin Li, Jian Shi, Jie Hu et al.
The growth of microorganisms is often confined in restricting geometries. In this work, we designed a device to study the growth propagation of budding yeast along linear arrays of microfluidic chambers. Vacuum assisted cell loading was used to seed cells of limited numbers in the up-most chambers o ... [Biomicrofluidics 5, 044118 (2011)] published Fri Dec 16, 2011.

Evaluation of bladder microvasculature with high-resolution photoacoustic imaging

Zhixing Xie, William Roberts, Paul Carson, Xiaojun Liu, Chao Tao et al.
We explored the potential of an emerging laser-based technology, photoacoustic imaging (PAI), for bladder cancer diagnosis through high-resolution imaging of microvasculature in the bladder tissues. Imaging results from ex vivo canine bladders demonstrated the excellent ability of PAI in mapping thr ... [Opt. Lett. 36, 4815 (2011)] published Tue Dec 20, 2011.

Erratum: Self-organized criticality as Witten-type topological field theory with spontaneously broken Becchi-Rouet-Stora-Tyutin symmetry [Phys. Rev. E 83, 051129 (2011)]

Igor V. Ovchinnikov
Abstract not available. [Phys. Rev. E 84, 069904 ] published .

Energy landscape of the reactions governing the Na deeply occluded state of the Na/K-ATPase in the giant axon of the Humboldt squid

Juan P. Castillo, Daniela De Giorgis, Daniel Basilio, David C. Gadsby, Joshua J. C. Rosenthal et al.
The Na/K pump is a nearly ubiquitous membrane protein in animal cells that uses the free energy of ATP hydrolysis to alternatively export 3Na from the cell and import 2K per cycle. This exchange of ions produces a steady-state outwardly directed current, which is proportional in magnitude to the tu ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20556 (2011)] published Thu Dec 22, 2011.

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events

Min K. Roh, Bernie J. Daigle, Jr., Dan T. Gillespie, and Linda R. Petzold
In recent years there has been substantial growth in the development of algorithms for characterizing rare events in stochastic biochemical systems. Two such algorithms, the state-dependent weighted stochastic simulation algorithm (swSSA) and the doubly weighted SSA (dwSSA) are extensions of the wei ... [J. Chem. Phys. 135, 234108 (2011)] published Tue Dec 20, 2011.

Architecture of human telomerase RNA

Qi Zhang, Nak-Kyoon Kim, and Juli Feigon
Telomerase is a unique reverse transcriptase that catalyzes the addition of telomere DNA repeats onto the 3' ends of linear chromosomes and plays a critical role in maintaining genome stability. Unlike other reverse transcriptases, telomerase is unique in that it is a ribonucleoprotein complex, whe ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20325 (2011)] published Thu Dec 22, 2011.

Vulnerability to paroxysmal oscillations in delayed neural networks: A basis for nocturnal frontal lobe epilepsy?

Austin Quan, Ivan Osorio, Toru Ohira, and John Milton
Resonance can occur in bistable dynamical systems due to the interplay between noise and delay (tau) in the absence of a periodic input. We investigate resonance in a two-neuron model with mutual time-delayed inhibitory feedback. For appropriate choices of the parameters and inputs three fixed-point ... [Chaos 21, 047512 (2011)] published Thu Dec 29, 2011.

Continuous-time random walks that alter environmental transport properties

C. Angstmann and B. I. Henry
We consider continuous-time random walks (CTRWs) in which the walkers have a finite probability to alter the waiting-time and/or step-length transport properties of their environment, resulting in possibly transient anomalous diffusion. We refer to these CTRWs as transmogrifying continuous-time rand ... [Phys. Rev. E 84, 061146 ] published .

Tweedie convergence: A mathematical basis for Taylor's power law, 1/f noise, and multifractality

Wayne S. Kendal and Bent Jorgensen
Plants and animals of a given species tend to cluster within their habitats in accordance with a power function between their mean density and the variance. This relationship, Taylor's power law, has been variously explained by ecologists in terms of animal behavior, interspecies interactions, demog ... [Phys. Rev. E 84, 066120 ] published .

Simulations of driven and reconstituting lattice gases

M. D. Grynberg
We discuss stationary aspects of a set of driven lattice gases in which hard-core particles with spatial extent, covering more than one lattice site, diffuse and reconstruct in one dimension under nearest-neighbor interactions. As in the uncoupled case [M. Barma et al., J. Phys.: Condens. Matter 19, ... [Phys. Rev. E 84, 061145 ] published .

Unstable periodic orbits and noise in chaos computing

Behnam Kia, Anna Dari, William L. Ditto, and Mark L. Spano
Different methods to utilize the rich library of patterns and behaviors of a chaotic system have been proposed for doing computation or communication. Since a chaotic system is intrinsically unstable and its nearby orbits diverge exponentially from each other, special attention needs to be paid to t ... [Chaos 21, 047520 (2011)] published Thu Dec 29, 2011.

Correlation transfer in stochastically driven neural oscillators over long and short time scales

Aushra Abouzeid and Bard Ermentrout
In the absence of synaptic coupling, two or more neural oscillators may become synchronized by virtue of the statistical correlations in their noisy input streams. Recent work has shown that the degree of correlation transfer from input currents to output spikes depends not only on intrinsic oscilla ... [Phys. Rev. E 84, 061914 ] published .

Noise-induced precursors of tonic-to-bursting transitions in hypothalamic neurons and in a conductance-based model

Hans A. Braun, Justus Schwabedal, Mathias Dewald, Christian Finke, Svetlana Postnova et al.
The dynamics of neurons is characterized by a variety of different spiking patterns in response to external stimuli. One of the most important transitions in neuronal response patterns is the transition from tonic firing to burst discharges, i.e., when the neuronal activity changes from single spike ... [Chaos 21, 047509 (2011)] published Thu Dec 29, 2011.

Synchronization analysis of voltage-sensitive dye imaging during focal seizures in the rat neocortex

Daisuke Takeshita and Sonya Bahar
Seizures are often assumed to result from an excess of synchronized neural activity. However, various recent studies have suggested that this is not necessarily the case. We investigate synchronization during focal neocortical seizures induced by injection of 4-aminopyridine (4AP) in the rat neocort ... [Chaos 21, 047506 (2011)] published Thu Dec 29, 2011.

Eikonal-based initiation of fibrillatory activity in thin-walled cardiac propagation models

Antoine Herlin and Vincent Jacquemet
Reentrant arrhythmias can be simulated in electrophysiological models of electrical impulse propagation governed by a reaction-diffusion system. To facilitate the initiation of a large number of independent episodes of simulated arrhythmias with controllable level of complexity, a new approach is pr ... [Chaos 21, 043136 (2011)] published Thu Dec 22, 2011.

Multivariate multiscale entropy: A tool for complexity analysis of multichannel data

Mosabber Uddin Ahmed and Danilo P. Mandic
This work generalizes the recently introduced univariate multiscale entropy (MSE) analysis to the multivariate case. This is achieved by introducing multivariate sample entropy (MSampEn) in a rigorous way, in order to account for both within- and cross-channel dependencies in multiple data channels, ... [Phys. Rev. E 84, 061918 ] published .

Pulmonary diffusional screening and the scaling laws of mammalian metabolic rates

Chen Hou and Michael Mayo
Theoretical considerations suggest that the mammalian metabolic rate is linearly proportional to the surface areas of mitochondria, capillary, and alveolar membranes. However, the scaling exponents of these surface areas to the mammals' body mass (approximately 0.91) are higher than exponents of the ... [Phys. Rev. E 84, 061915 ] published .

Deionization shocks in microstructures

Ali Mani and Martin Z. Bazant
Salt transport in bulk electrolytes is limited by diffusion and advection, but in microstructures with charged surfaces (e.g., microfluidic devices, porous media, soils, or biological tissues) surface conduction and electro-osmotic flow also contribute to ionic fluxes. For small applied voltages, th ... [Phys. Rev. E 84, 061504 ] published .

Dynamic model of flexible phytoplankton nutrient uptake

Juan A. Bonachela, Michael Raghib, and Simon A. Levin
The metabolic machinery of marine microbes can be remarkably plastic, allowing organisms to persist under extreme nutrient limitation. With some exceptions, most theoretical approaches to nutrient uptake in phytoplankton are largely dominated by the classic MichaelisMenten (MM) uptake functional fo ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20633 (2011)] published Thu Dec 22, 2011.

A common repressor pool results in indeterminacy of extrinsic noise

Michail Stamatakis, Rhys M. Adams, and Gabor Balazsi
For just over a decade, stochastic gene expression has been the focus of many experimental and theoretical studies. It is now widely accepted that noise in gene expression can be decomposed into extrinsic and intrinsic components, which have orthogonal contributions to the total noise. Intrinsic noi ... [Chaos 21, 047523 (2011)] published Thu Dec 29, 2011.

Nonlinear dynamics of skin potentials in the electrosensory paddlefish

Michael H. Hofmann and Lon A. Wilkens
It is known that steady skin potentials are present in fishes due to chloride pumps in the gills and in the skin. We have found previously that these skin potentials can fluctuate and oscillate in the electrosensory paddlefish. Here we show that larger, discharge like potentials can be triggered by ... [Chaos 21, 047504 (2011)] published Thu Dec 29, 2011.

Stochastic resonance on a modular neuronal network of small-world subnetworks with a subthreshold pacemaker

Haitao Yu, Jiang Wang, Chen Liu, Bin Deng, and Xile Wei
We study the phenomenon of stochastic resonance on a modular neuronal network consisting of several small-world subnetworks with a subthreshold periodic pacemaker. Numerical results show that the correlation between the pacemaker frequency and the dynamical response of the network is resonantly depe ... [Chaos 21, 047502 (2011)] published Thu Dec 29, 2011.

Logical stochastic resonance with correlated internal and external noises in a synthetic biological logic block

Anna Dari, Behnam Kia, Adi R. Bulsara, and William L. Ditto
Following the advent of synthetic biology, several gene networks have been engineered to emulate digital devices, with the ability to program cells for different applications. In this work, we adapt the concept of logical stochastic resonance to a synthetic gene network derived from a bacteriophage ... [Chaos 21, 047521 (2011)] published Thu Dec 29, 2011.

Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods

Rajesh Ramaswamy and Ivo F. Sbalzarini
Stochastic reaction-diffusion systems frequently exhibit behavior that is not predicted by deterministic simulation models. Stochastic simulation methods, however, are computationally expensive. We present a more efficient stochastic reaction-diffusion simulation algorithm that samples realizations ... [J. Chem. Phys. 135, 244103 (2011)] published Fri Dec 23, 2011.

Local adaptation of an introduced transgenic insect fungal pathogen due to new beneficial mutations

Sibao Wang, Tammatha R. O'Brien, Monica Pava-Ripoll, and Raymond J. St. Leger
Genetically modified Metarhizium spp represent a major new arsenal for combating insect pests and insect-borne diseases. However, for these tools to be used safely and effectively, we need a much better understanding of their evolutionary potential and invasion ecology. In order to model natural as ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20449 (2011)] published Thu Dec 22, 2011.

Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase

Patrick O'Donoghue, Kelly Sheppard, Osamu Nureki, and Dieter Soll
The specificity of most aminoacyl-tRNA synthetases for an amino acid and cognate tRNA pair evolved before the divergence of the three domains of life. Glutaminyl-tRNA synthetase (GlnRS) evolved later and is derived from the archaeal-type nondiscriminating glutamyl-tRNA synthetase (GluRS), an enzyme ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20485 (2011)] published Thu Dec 22, 2011.

Cooperation, structure, and hierarchy in multiadaptive games

Sungmin Lee, Petter Holme, and Zhi-Xi Wu
Game-theoretical models where the rules of the game and the interaction structure both coevolve with the game dynamicsmultiadaptive gamescapture very flexible situations where cooperation among selfish agents can emerge. In this work, we will discuss a multiadaptive model presented in a recent Lette ... [Phys. Rev. E 84, 061148 ] published .

Effects of punishment in a mobile population playing the prisoner's dilemma game

Daniel R. Amor and Joaquim Fort
We deal with a system of prisoner's dilemma players undergoing continuous motion in a two-dimensional plane. In contrast to previous work, we introduce altruistic punishment after the game. We find punishing only a few of the cooperator-defector interactions is enough to lead the system to a coopera ... [Phys. Rev. E 84, 066115 ] published .

Phase transition in an exactly solvable extinction model

Debarshee Bagchi and P. K. Mohanty
We introduce a model of biological evolution in which species evolve in response to biotic interactions and fluctuating environmental stress. The species may either become extinct or mutate to acquire a new fitness value when the effective stress level is greater than their individual fitness. The m ... [Phys. Rev. E 84, 061921 ] published .

Autoinhibition and phosphorylation-induced activation mechanisms of human cancer and autoimmune disease-related E3 protein Cbl-b

Yoshihiro Kobashigawa, Akira Tomitaka, Hiroyuki Kumeta, Nobuo N. Noda, Masaya Yamaguchi et al.
Cbl-b is a RING-type E3 ubiquitin ligase that functions as a negative regulator of T-cell activation and growth factor receptor and nonreceptor-type tyrosine kinase signaling. Cbl-b dysfunction is related to autoimmune diseases and cancers in humans. However, the molecular mechanism regulating its ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20579 (2011)] published Thu Dec 22, 2011.

Maintenance of tumor initiating cells of defined genetic composition by nucleostemin

Naoko Okamoto, Mami Yasukawa, Christine Nguyen, Vivi Kasim, Yoshiko Maida et al.
Recent work has identified a subset of cells resident in tumors that exhibit properties similar to those found in normal stem cells. Such cells are highly tumorigenic and may be involved in resistance to treatment. However, the genes that regulate the tumor initiating cell (TIC) state are unknown. ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20388 (2011)] published Thu Dec 22, 2011.

Molecular basis for the differential use of glucose and glutamine in cell proliferation as revealed by synchronized HeLa cells

Sergio L. Colombo, Miriam Palacios-Callender, Nanci Frakich, Saul Carcamo, Istvan Kovacs et al.
During cell division, the activation of glycolysis is tightly regulated by the action of two ubiquitin ligases, anaphase-promoting complex/cyclosomeCdh1 (APC/C-Cdh1) and SKP1/CUL-1/F-box proteinbeta-transducin repeat-containing protein (SCF-beta-TrCP), which control the transient appearance and met ... [Proc. Natl. Acad. Sci. U.S.A. 108, 21069 (2011)] published Thu Dec 29, 2011.

Notch1 regulates the expression of the multidrug resistance gene ABCC1/MRP1 in cultured cancer cells

Sungpil Cho, Meiling Lu, Xiaolong He, Pui-Lai Rachel Ee, Uppoor Bhat et al.
Multidrug resistance (MDR) is a barrier to successful cancer chemotherapy. Although MDR is associated with overexpression of ATP-binding cassette (ABC) membrane transporters, mechanisms behind their up-regulation are not entirely understood. The cleaved form of the Notch1 protein, intracellular Not ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20778 (2011)] published Thu Dec 22, 2011.

Multiple stromal populations contribute to pulmonary fibrosis without evidence for epithelial to mesenchymal transition

Jason R. Rock, Christina E. Barkauskas, Michael J. Cronce, Yan Xue, Jeffrey R. Harris et al.
There are currently few treatment options for pulmonary fibrosis. Innovations may come from a better understanding of the cellular origin of the characteristic fibrotic lesions. We have analyzed normal and fibrotic mouse and human lungs by confocal microscopy to define stromal cell populations with ... [Proc. Natl. Acad. Sci. U.S.A. 108, E1475 (2011)] published Thu Dec 29, 2011.

Fabrication of immunosensor microwell arrays from gold compact discs for detection of cancer biomarker proteins

Chi K. Tang, Abhay Vaze, and James F. Rusling
A simple method is reported to fabricate gold arrays featuring microwells surrounding 8-electrodes from gold compact discs (CDs) for less than $0.2 per chip. Integration of these disposable gold CD array chips with microfluidics provided inexpensive immunoarrays that were used to measure a cancer bi ... [Lab Chip 12, 281 (2011)] published Fri Dec 16, 2011.

Dielectric barrier discharge plasma in Ar/O promoting apoptosis behavior in A549 cancer cells

Jun Huang, Hui Li, Wei Chen, Guo-Hua Lv, Xing-Quan Wang et al.
The Ar/O plasma needle in the induction of A549 cancer cells apoptosis process is studied by means of real-time observation. The entire process of programmed cell death is observed. The typical morphological changes of A549 apoptosis are detected by 4[prime], 6-diamidino-2-phenylindole staining, for ... [Appl. Phys. Lett. 99, 253701 (2011)] published Mon Dec 19, 2011.

Crystal structure of the mucosa-associated lymphoid tissue lymphoma translocation 1 (MALT1) paracaspase region

Jong W. Yu, Philip D. Jeffrey, Jun Yong Ha, Xiaolu Yang, and Yigong Shi
The mucosa-associated lymphoid tissue lymphoma translocation 1 (MALT1) paracaspase, a key component of the Carma1/Bcl10/MALT1 signalosome, is critical for NF-kappaB signaling in multiple contexts. MALT1 is thought to function as a scaffold and protease to promote signaling; however, the biochemical ... [Proc. Natl. Acad. Sci. U.S.A. 108, 21004 (2011)] published Thu Dec 29, 2011.

Photoactivated cationic alkyl-substituted porphyrin binding to g4-RNA in the 5[prime]-UTR of KRAS oncogene represses translation

Mariangela Faudale, Susanna Cogoi, and Luigi E. Xodo
The KRAS transcript is characterized by a 192-nt 5[prime]-UTR containing repetitive runs of two-guanines which can fold in several G-quadruplexes. These folded structures have a high affinity for the cationic porphyrin tri-meso(N-methyl-4-pyridyl), meso(N-tetradecyl-4-pyridyl) porphine (TMPyP4-C14), ... [Chem. Commun. 48, 874 (2011)] published Fri Dec 16, 2011.

Non-Markovian models for migration-proliferation dichotomy of cancer cells: Anomalous switching and spreading rate

Sergei Fedotov, Alexander Iomin, and Lev Ryashko
Proliferation and migration dichotomy of the tumor cell invasion is examined within two non-Markovian models. We consider the tumor spheroid, which consists of the tumor core with a high density of cells and the outer invasive zone. We distinguish two different regions of the outer invasive zone and ... [Phys. Rev. E 84, 061131 ] published .

Erratum: Dynamics of a genetic toggle switch at the nucleotide and codon levels [Phys. Rev. E 84, 031903 (2011)]

Ilya Potapov, Jason Lloyd-Price, Olli Yli-Harja, and Andre S. Ribeiro
Abstract not available. [Phys. Rev. E 84, 069903 ] published .

Human monocytes are severely impaired in base and DNA double-strand break repair that renders them vulnerable to oxidative stress

Martina Bauer, Michael Goldstein, Markus Christmann, Huong Becker, Daniel Heylmann et al.
Monocytes are key players in the immune system. Crossing the blood barrier, they infiltrate tissues and differentiate into (i) macrophages that fight off pathogens and (ii) dendritic cells (DCs) that activate the immune response. A hallmark of monocyte/macrophage activation is the generation of rea ... [Proc. Natl. Acad. Sci. U.S.A. 108, 21105 (2011)] published Thu Dec 29, 2011.

DNA double-strand breaks induced by high NaCl occur predominantly in gene deserts

Natalia I. Dmitrieva, Kairong Cui, Daniil A. Kitchaev, Keji Zhao, and Maurice B. Burg
High concentration of NaCl increases DNA breaks both in cell culture and in vivo. The breaks remain elevated as long as NaCl concentration remains high and are rapidly repaired when the concentration is lowered. The exact nature of the breaks, and their location, has not been entirely clear, and it ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20796 (2011)] published Thu Dec 22, 2011.

Retrotransposition is associated with genome instability during chronological aging

Patrick H. Maxwell, William C. Burhans, and M. Joan Curcio
Genetic damage through mutations and genome rearrangements has been hypothesized to contribute to aging. The specific mechanisms responsible for age-induced increases in mutation and chromosome rearrangement frequencies and a potential causative role for DNA damage in aging are under active investi ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20376 (2011)] published Thu Dec 22, 2011.

Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression

James M. Carothers, Jonathan A. Goler, Darmawi Juminaga, and Jay D. Keasling
The models and simulation tools available to design functionally complex synthetic biological devices are very limited. We formulated a design-driven approach that used mechanistic modeling and kinetic RNA folding simulations to engineer RNA-regulated genetic devices that control gene expression. Ri ... [Science 334, 1716 (2011)] published Thu Dec 22, 2011.

A widespread class of reverse transcriptase-related cellular genes

Eugene A. Gladyshev and Irina R. Arkhipova
Reverse transcriptases (RTs) polymerize DNA on RNA templates. They fall into several structurally related but distinct classes and form an assemblage of RT-like enzymes that, in addition to RTs, also includes certain viral RNA-dependent RNA polymerases (RdRP) synthesizing RNA on RNA templates. It i ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20311 (2011)] published Thu Dec 22, 2011.

DNA-binding factors shape the mouse methylome at distal regulatory regions

Michael B. Stadler, Rabih Murr, Lukas Burger, Robert Ivanek, Florian Lienert et al.
Methylation of cytosines is an essential epigenetic modification in mammalian genomes, yet the rules that govern methylation patterns remain largely elusive. To gain insights into this process, we generated base-pair-resolution mouse methylomes in stem cells and neuronal progenitors. Advanced quanti ... [Nature 480, 490 (2011)] published Thu Dec 22, 2011.

Mismatch Repair, But Not Heteroduplex Rejection, Is Temporally Coupled to DNA Replication

Hans Hombauer, Anjana Srivatsan, Christopher D. Putnam, and Richard D. Kolodner
In eukaryotes, it is unknown whether mismatch repair (MMR) is temporally coupled to DNA replication and how strand-specific MMR is directed. We fused Saccharomyces cerevisiae MSH6 with cyclins to restrict the availability of the Msh2-Msh6 mismatch recognition complex to either S phase or G2/M phase ... [Science 334, 1713 (2011)] published Thu Dec 22, 2011.

High-efficiency homologous recombination in the oil-producing alga Nannochloropsis sp.

Oliver Kilian, Christina S. E. Benemann, Krishna K. Niyogi, and Bertrand Vick
Algae have reemerged as potential next-generation feedstocks for biofuels, but strain improvement and progress in algal biology research have been limited by the lack of advanced molecular tools for most eukaryotic microalgae. Here we describe the development of an efficient transformation method f ... [Proc. Natl. Acad. Sci. U.S.A. 108, 21265 (2011)] published Thu Dec 29, 2011.

Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways

Jian Wu, Yuchen Jiao, Marco Dal Molin, Anirban Maitra, Roeland F. de Wilde et al.
More than 2% of adults harbor a pancreatic cyst, a subset of which progresses to invasive lesions with lethal consequences. To assess the genomic landscapes of neoplastic cysts of the pancreas, we determined the exomic sequences of DNA from the neoplastic epithelium of eight surgically resected cys ... [Proc. Natl. Acad. Sci. U.S.A. 108, 21188 (2011)] published Thu Dec 29, 2011.

Genome diversity in wild grasses under environmental stress

Timothy L. Fitzgerald, Frances M. Shapter, Stuart McDonald, Daniel L. E. Waters, Ian H. Chivers et al.
Patterns of diversity distribution in the Isa defense locus in wild-barley populations suggest adaptive selection at this locus. The extent to which environmental selection may act at additional nuclear-encoded defense loci and within the whole chloroplast genome has now been examined by analyses i ... [Proc. Natl. Acad. Sci. U.S.A. 108, 21140 (2011)] published Thu Dec 29, 2011.

The genomic binding sites of a noncoding RNA

Matthew D. Simon, Charlotte I. Wang, Peter V. Kharchenko, Jason A. West, Brad A. Chapman et al.
Long noncoding RNAs (lncRNAs) have important regulatory roles and can function at the level of chromatin. To determine where lncRNAs bind to chromatin, we developed capture hybridization analysis of RNA targets (CHART), a hybridization-based technique that specifically enriches endogenous RNAs alon ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20497 (2011)] published Thu Dec 22, 2011.

The Medicago genome provides insight into the evolution of rhizobial symbioses

Nevin D. Young, Frdric Debell, Giles E. D. Oldroyd, Rene Geurts, Steven B. Cannon et al.
Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabid ... [Nature 480, 520 (2011)] published Thu Dec 22, 2011.

Scale-free duplication dynamics: A model for ultraduplication

M. V. Koroteev and J. Miller
Empirical studies of the genome-wide length distribution of duplicated sequences have revealed an algebraic tail common to nearly all clades. The decay of the tail is often well approximated by a single exponent that takes values within a limited range. We propose and study here scale-free duplicati ... [Phys. Rev. E 84, 061919 ] published .

Room-temperature, atmospheric plasma needle reduces adenovirus gene expression in HEK 293A host cells

Z. Xiong, X. Lu, Y. Cao, Q. Ning, K. Ostrikov et al.
Room-temperature, atmospheric-pressure plasma needle treatment is used to effectively minimize the adenovirus (AdV) infectivity as quantified by the dramatic reduction of its gene expression in HEK 293A primary human embryonic kidney cells studied by green fluorescent protein imaging. The AdV titer ... [Appl. Phys. Lett. 99, 253703 (2011)] published Tue Dec 20, 2011.

Transcriptional proofreading in dense RNA polymerase traffic

Mamata Sahoo and Stefan Klumpp
The correction of errors during transcription involves the diffusive backward translocation (backtracking) of RNA polymerases (RNAPs) on the DNA. A trailing RNAP on the same template can interfere with backtracking as it progressively restricts the space that is available for backward translocation ... [EPL 96, 60004 (2011)] published Thu Dec 22, 2011.

Loss of synchronization in complex neuronal networks with delay

J. Lehnert, T. Dahms, P. Hvel, and E. Schll
We investigate the stability of synchronization in networks of delay-coupled excitable neural oscillators. On the basis of the master stability function formalism, we demonstrate that synchronization is always stable for excitatory coupling independently of the delay and coupling strength. Superimpo ... [EPL 96, 60013 (2011)] published Thu Dec 22, 2011.

Communities, modules and large-scale structure in networks

M. E. J. Newman
Networks, also called graphs by mathematicians, provide a useful abstraction of the structure of many complex systems, ranging from social systems and computer networks to biological networks and the state spaces of physical systems. In the past decade there have been significant advances in experim ... [Nature Phys. 8, 25 (2011)] published Thu Dec 22, 2011.

Control of delay-induced oscillation death by coupling phase in coupled oscillators

Wei Zou, Jianquan Lu, Yang Tang, Chengjian Zhang, and Jurgen Kurths
A coupling phase is deemed to be crucial in stabilizing behavior in nonlinear systems. In this paper, we study how the coupling phase influences the delay-induced oscillation death (OD) in coupled oscillators. The OD boundaries are identified analytically even in the presence of the coupling phase. ... [Phys. Rev. E 84, 066208 ] published .

Variability of spatio-temporal patterns in non-homogeneous rings of spiking neurons

Serhiy Yanchuk, Przemyslaw Perlikowski, Oleksandr V. Popovych, and Peter A. Tass
We show that a ring of unidirectionally delay-coupled spiking neurons may possess a multitude of stable spiking patterns and provide a constructive algorithm for generating a desired spiking pattern. More specifically, for a given time-periodic pattern, in which each neuron fires once within the pat ... [Chaos 21, 047511 (2011)] published Thu Dec 29, 2011.

Key role of time-delay and connection topology in shaping the dynamics of noisy genetic regulatory networks

X. L. Yang, D. V. Senthilkumar, Z. K. Sun, and J. Kurths
This paper focuses on a paced genetic regulatory small-world network with time-delayed coupling. How the dynamical behaviors including temporal resonance and spatial synchronization evolve under the influence of time-delay and connection topology is explored through numerical simulations. We reveal ... [Chaos 21, 047522 (2011)] published Thu Dec 29, 2011.

A Cultured Greigite-Producing Magnetotactic Bacterium in a Novel Group of Sulfate-Reducing Bacteria

Christopher T. Lefvre, Nicolas Menguy, Fernanda Abreu, Ulysses Lins, Mihly Psfai et al.
Magnetotactic bacteria contain magnetosomesintracellular, membrane-bounded, magnetic nanocrystals of magnetite (Fe3O4) or greigite (Fe3S4)that cause the bacteria to swim along geomagnetic field lines. We isolated a greigite-producing magnetotactic bacterium from a brackish spring in Death Valley Nat ... [Science 334, 1720 (2011)] published Thu Dec 22, 2011.

Fast wandering of slow birds

John Toner
I study a single slow bird moving with a flock of birds of a different and faster (or slower) species. I find that every species of flocker has a characteristic speed gamma[not-equal]v, where v is the mean speed of the flock such that if the speed v of the slow bird equals gamma, it will randomly wa ... [Phys. Rev. E 84, 061913 ] published .

Coherence depression in stochastic excitable systems with two-frequency forcing

Na Yu and Andre Longtin
We study the response of two generic neuron models, the leaky integrate-and-fire (LIF) model and the leaky integrate-and-fire model with dynamic threshold (LIFDT) (i.e., with memory) to a stimulus consisting of two sinusoidal drives with incommensurate frequency, an amplitude modulation (envelope) n ... [Chaos 21, 047507 (2011)] published Thu Dec 29, 2011.

Velocity-jump models with crowding effects

Katrina K. Treloar, Matthew J. Simpson, and Scott W. McCue
Velocity-jump processes are discrete random-walk models that have many applications including the study of biological and ecological collective motion. In particular, velocity-jump models are often used to represent a type of persistent motion, known as a run and tumble, that is exhibited by some is ... [Phys. Rev. E 84, 061920 ] published .

Genesis of two-dimensional patterns in cross-gradient fields

L. M. Pismen and D. S. A. Simakov
Tissue morphogenesis is controlled by the two-dimensional patterning of gene expression in epithelial layers, that determines cell fates. The mechanisms of pattern formation involve intracellular regulatory networks controlled by paracrine and autocrine signaling. We develop a general logical scheme ... [Phys. Rev. E 84, 061917 ] published .

Npas4 Regulates a Transcriptional Program in CA3 Required for Contextual Memory Formation

Kartik Ramamoorthi, Robin Fropf, Gabriel M. Belfort, Helen L. Fitzmaurice, Ross M. McKinney et al.
The rapid encoding of contextual memory requires the CA3 region of the hippocampus, but the necessary genetic pathways remain unclear. We found that the activity-dependent transcription factor Npas4 regulates a transcriptional program in CA3 that is required for contextual memory formation. Npas4 wa ... [Science 334, 1669 (2011)] published Thu Dec 22, 2011.

Mouse B-Type Lamins Are Required for Proper Organogenesis But Not by Embryonic Stem Cells

Youngjo Kim, Alexei A. Sharov, Katie McDole, Melody Cheng, Haiping Hao et al.
B-type lamins, the major components of the nuclear lamina, are believed to be essential for cell proliferation and survival. We found that mouse embryonic stem cells (ESCs) do not need any lamins for self-renewal and pluripotency. Although genome-wide lamin-B binding profiles correlate with reduced ... [Science 334, 1706 (2011)] published Thu Dec 22, 2011.

Cryptochromes mediate rhythmic repression of the glucocorticoid receptor

Katja A. Lamia, Stephanie J. Papp, Ruth T. Yu, Grant D. Barish, N. Henriette Uhlenhaut et al.
Mammalian metabolism is highly circadian and major hormonal circuits involving nuclear hormone receptors display interlinked diurnal cycling. However, mechanisms that logically explain the coordination of nuclear hormone receptors and the clock are poorly understood. Here we show that two circadian ... [Nature 480, 552 (2011)] published Thu Dec 22, 2011.

First passage time distribution of chaperone driven polymer translocation through a nanopore: Homopolymer and heteropolymer cases

Rouhollah Haji Abdolvahab, Ralf Metzler, and Mohammad Reza Ejtehadi
Combining the advection-diffusion equation approach with Monte Carlo simulations we study chaperone driven polymer translocation of a stiff polymer through a nanopore. We demonstrate that the probability density function of first passage times across the pore depends solely on the Peclet number, a d ... [J. Chem. Phys. 135, 245102 (2011)] published Fri Dec 23, 2011.

Sensory coding in oscillatory electroreceptors of paddlefish

Alexander B. Neiman and David F. Russell
Coherence and information theoretic analyses were applied to quantitate the response properties and the encoding of time-varying stimuli in paddlefish electroreceptors (ERs), studied in vivo. External electrical stimuli were Gaussian noise waveforms of varied frequency band and strength, including n ... [Chaos 21, 047505 (2011)] published Thu Dec 29, 2011.

Stiffness and strength of suture joints in nature

Yaning Li, Christine Ortiz, and Mary C. Boyce
Suture joints are remarkable mechanical structures found throughout nature composed of compliant interlocking seams connecting stiffer components. This study investigates the underlying mechanisms and the role of geometry governing the unique mechanical behavior of suture joints. Analytical and nume ... [Phys. Rev. E 84, 062904 ] published .

Biomaterial surface modifications can dominate cellsubstrate mechanics: the impact of PDMS plasma treatment on a quantitative assay of cell stiffness

G. Bartalena, Y. Loosli, T. Zambelli, and J. G. Snedeker
Polydimethylsiloxane (PDMS) is a bioinert synthetic polymer with tunable elastic properties that is commonly used as a cell culture substrate. Although plasma treatments are widely used to bio-functionalize otherwise hydrophobic PDMS surfaces, plasma altered surface mechanical properties and implica ... [Soft Matter 8, 673 (2011)] published Fri Dec 16, 2011.

Direct Redox Regulation of F-Actin Assembly and Disassembly by Mical

Ruei-Jiun Hung, Chi W. Pak, and Jonathan R. Terman
Different types of cell behavior, including growth, motility, and navigation, require actin proteins to assemble into filaments. Here, we describe a biochemical process that was able to disassemble actin filaments and limit their reassembly. Actin was a specific substrate of the multidomain oxidatio ... [Science 334, 1710 (2011)] published Thu Dec 22, 2011.

Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase

Nozomi Ando, Edward J. Brignole, Christina M. Zimanyi, Michael A. Funk, Kenichi Yokoyama et al.
Essential for DNA biosynthesis and repair, ribonucleotide reductases (RNRs) convert ribonucleotides to deoxyribonucleotides via radical-based chemistry. Although long known that allosteric regulation of RNR activity is vital for cell health, the molecular basis of this regulation has been enigmatic ... [Proc. Natl. Acad. Sci. U.S.A. 108, 21046 (2011)] published Thu Dec 29, 2011.

Testing resonating vector strength: Auditory system, electric fish, and noise

J. Leo van Hemmen, Andre Longtin, and Andreas N. Vollmayr
Quite often a response to some input with a specific frequency nu can be described through a sequence of discrete events. Here, we study the synchrony vector, whose length stands for the vector strength, and in doing so focus on neuronal response in terms of spike times. The latter are supposed to b ... [Chaos 21, 047508 (2011)] published Thu Dec 29, 2011.

Asymmetry of red blood cell motions in a microchannel with a diverging and converging bifurcation

Vladimir Leble, Rui Lima, Ricardo Dias, Carla Fernandes, Takuji Ishikawa et al.
In microcirculation, red blood cells (RBCs) flowing through bifurcations may deform considerably due to combination of different phenomena that happen at the micro-scale level, such as: attraction effect, high shear, and extensional stress, all of which may influence the rheological properties and f ... [Biomicrofluidics 5, 044120 (2011)] published Fri Dec 23, 2011.

Actin disassembly clock determines shape and speed of lamellipodial fragments

Noa Ofer, Alexander Mogilner, and Kinneret Keren
A central challenge in motility research is to quantitatively understand how numerous molecular building blocks self-organize to achieve coherent shape and movement on cellular scales. A classic example of such self-organization is lamellipodial motility in which forward translocation is driven by ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20394 (2011)] published Thu Dec 22, 2011.

Forces and Torques on Rotating Spirochete Flagella

Jing Yang, Greg Huber, and Charles W. Wolgemuth
Spirochetes are a unique group of motile bacteria that are distinguished by their helical or flat-wave shapes and the location of their flagella, which reside within the tiny space between the bacterial cell wall and the outer membrane (the periplasm). In Borrelia burgdorferi, rotation of the flagel ... [Phys. Rev. Lett. 107, 268101 ] published .

Early integrin binding to Arg-Gly-Asp peptide activates actin polymerization and contractile movement that stimulates outward translocation

Cheng-han Yu, Jaslyn Bee Khuan Law, Mona Suryana, Hong Yee Low, and Michael P. Sheetz
Integrin-mediated adhesions are critical for stem cell differentiation, cancer metastasis, and the immune response [Hynes RO (2009) Science 326:12161219]. However, the mechanisms of early adhesion formation remain unclear, especially the effects of lateral clustering of integrins and the role of th ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20585 (2011)] published Thu Dec 22, 2011.

Cell Motility Resulting from Spontaneous Polymerization Waves

K. Doubrovinski and K. Kruse
The crawling of cells on a substrate is in many cases driven by the actin cytoskeleton. How actin filaments and associated proteins are organized to generate directed motion is still poorly understood. Recent experimental observations suggest that spontaneous cytoskeletal waves might orchestrate the ... [Phys. Rev. Lett. 107, 258103 ] published .

Remodeling of actin filaments by ADF/cofilin proteins

Vitold E. Galkin, Albina Orlova, Dmitri S. Kudryashov, Alexander Solodukhin, Emil Reisler et al.
Cofilin/ADF proteins play key roles in the dynamics of actin, one of the most abundant and highly conserved eukaryotic proteins. We used cryoelectron microscopy to generate a 9-A resolution three-dimensional reconstruction of cofilin-decorated actin filaments, the highest resolution achieved for a ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20568 (2011)] published Thu Dec 22, 2011.

Systematic control of protein interactions for systems biology

Nitin Bhardwaj, Declan Clarke, and Mark Gerstein
Abstract not available. [Proc. Natl. Acad. Sci. U.S.A. 108, 20279 (2011)] published Thu Dec 22, 2011.

A statistical mechanical approach to protein aggregation

John S. Schreck and Jian-Min Yuan
We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for the understanding and treatment of neurodegenerative disease ... [J. Chem. Phys. 135, 235102 (2011)] published Tue Dec 20, 2011.

Telomerase regulatory subunit Est3 in two Candida species physically interacts with the TEN domain of TERT and telomeric DNA

Wei-Feng Yen, Lidia Chico, Ming Lei, and Neal F. Lue
The yeast telomerase regulatory protein Est3 is required for telomere maintenance in vivo, and shares intriguing structural and functional similarities with the mammalian telomeric protein TPP1. Here we report our physical and functional characterizations of Est3 homologues from Candida parapsilosi ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20370 (2011)] published Thu Dec 22, 2011.

The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization

Gabor Pohl, Imre Jakli, Imre G. Csizmadia, Dora Papp, Garibotto Francisco Matias et al.
The initiation and progression of Alzheimer's disease is coupled to the oligo- and polymerization of amyloid peptides in the brain. Amyloid like aggregates of protein domains were found practically independent of their primary sequences. Thus, the driving force of the transformation from the origina ... [Phys. Chem. Chem. Phys. 14, 1507 (2011)] published Tue Dec 27, 2011.

Numerically exact, time-dependent treatment of vibrationally coupled electron transport in single-molecule junctions

Haobin Wang, Ivan Pshenichnyuk, Rainer Hartle, and Michael Thoss
The multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) theory within second quantization representation of the Fock space, a novel numerically exact methodology to treat many-body quantum dynamics for systems containing identical particles, is applied to study the effect of vibrational ... [J. Chem. Phys. 135, 244506 (2011)] published Thu Dec 29, 2011.

Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules

Dylan T. Burnette, Prabuddha Sengupta, Yuhai Dai, Jennifer Lippincott-Schwartz, and Bechara Kachar
Superresolution imaging techniques based on the precise localization of single molecules, such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), achieve high resolution by fitting images of single fluorescent molecules with a theoretical Gaus ... [Proc. Natl. Acad. Sci. U.S.A. 108, 21081 (2011)] published Thu Dec 29, 2011.

Functional importance of telomerase pseudoknot revealed by single-molecule analysis

Mariana Mihalusova, John Y. Wu, and Xiaowei Zhuang
Telomerase ribonucleoprotein (RNP) employs an RNA subunit to template the addition of telomeric repeats onto chromosome ends. Previous studies have suggested that a region of the RNA downstream of the template may be important for telomerase activity and that the region could fold into a pseudoknot ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20339 (2011)] published Thu Dec 22, 2011.

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

Parin Sripakdeevong, Wipapat Kladwang, and Rhiju Das
Atomic-accuracy structure prediction of macromolecules should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete sampling of a biopolymer's many degrees of freedom. We present herein a working hypothesis, called the "stepwise ansatz," for rec ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20573 (2011)] published Thu Dec 22, 2011.

The DNA three-way junction as a mould for tripartite chromophore assembly

Markus Probst, Daniel Wenger, Sarah M. Biner, and Robert Haner
The DNA three-way junction serves as a scaffold for the molecular organization of non-nucleosidic alkynylpyrene and perylenediimide chromophores located at the branch point of the structure. Depending on the composition of the tripartite assembly, the constructs possess distinct spectroscopic proper ... [Org. Biomol. Chem. 10, 755 (2011)] published Tue Dec 27, 2011.

DNA end processing by polynucleotide kinase/phosphatase

Matthew J. Schellenberg and R. Scott Williams
Abstract not available. [Proc. Natl. Acad. Sci. U.S.A. 108, 20855 (2011)] published Thu Dec 29, 2011.

Cotranscriptional folding kinetics of ribonucleic acid secondary structures

Peinan Zhao, Wenbing Zhang, and Shi-Jie Chen
We develop a systematic helix-based computational method to predict RNA folding kinetics during transcription. In our method, the transcription is modeled as stepwise process, where each step is the transcription of a nucleotide. For each step, the kinetics algorithm predicts the population kinetics ... [J. Chem. Phys. 135, 245101 (2011)] published Thu Dec 22, 2011.

The restoration of DNA structures by the drywet method

Junwye Lee, Rashid Amin, Byeonghoon Kim, Sang Jung Ahn, Keun Woo Lee et al.
Since DNA nanotechnology often requires water-based solution annealing processes, there are certain limitations on applying the results directly to physical devices which should be protected from the water treatment process during sample preparation. In an effort to overcome this problem, we develop ... [Soft Matter 8, 619 (2011)] published Fri Dec 16, 2011.

How a DNA Polymerase Clamp Loader Opens a Sliding Clamp

Brian A. Kelch, Debora L. Makino, Mike O'Donnell, and John Kuriyan
Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound ... [Science 334, 1675 (2011)] published Thu Dec 22, 2011.

High salt and DNA double-strand breaks

Christophe E. Redon and William M. Bonner
Abstract not available. [Proc. Natl. Acad. Sci. U.S.A. 108, 20281 (2011)] published Thu Dec 22, 2011.

Finite-enthalpy model parameters from DNA melting temperatures

G. Weber
Peyrard-Bishop (PB) models are used for the study of denaturation in DNA. Unfortunately, there is little connection of these models to linear nearest-neighbour models which are extensively used for the calculation of melting temperatures in biochemistry. Here we use the Joyeux-Buyukdagli (JB) model, ... [EPL 96, 68001 (2011)] published Thu Dec 22, 2011.

Controlling the conformations and transport of DNA by free energy landscaping

Elijah Shelton, Zhijun Jiang, Shutong Wang, and Derek Stein
We demonstrate free energy landscaping, a method for controlling the transport and conformations of DNA in nanofluidic devices with a nanotopography. A device that funnels molecules into traps where they adopt the shapes of letters illustrates the principle. We analyze how the nanotopography establi ... [Appl. Phys. Lett. 99, 263112 (2011)] published Fri Dec 30, 2011.

Dynamic metabolic labeling of DNA in vivo with arabinosyl nucleosides

Anne B. Neef and Nathan W. Luedtke
Commonly used metabolic labels for DNA, including 5-ethynyl-2'-deoxyuridine (EdU) and BrdU, are toxic antimetabolites that cause DNA instability, necrosis, and cell-cycle arrest. In addition to perturbing biological function, these properties can prevent metabolic labeling studies where subsequent ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20404 (2011)] published Thu Dec 22, 2011.

Gel electrophoresis of linear and star-branched DNA

Henry W. Lau and Lynden A. Archer
The electrophoretic mobility of double-stranded DNA in polyacrylamide gel is investigated using an activated hopping model for the transport of a charged object within a heterogeneous medium. The model is premised upon a representation of the DNA path through the gel matrix as a series of traps with ... [Phys. Rev. E 84, 061916 ] published .

Mean bubble formation time in DNA denaturation

K. Murthy and G. Schtz
Using the Poland-Scheraga free energy of the bubble size in a double-stranded DNA we propose a discrete stochastic dynamics for the number of base pairs N of an unzipped bubble. We derive a universal subdiffusive growth TA/(b+2)N for the mean formation time (MBFT) T of a bubble of size N. The amplit ... [EPL 96, 68003 (2011)] published Thu Dec 22, 2011.

Kinetic Monte Carlo method applied to nucleic acid hairpin folding

Ben Sauerwine and Michael Widom
Kinetic Monte Carlo on coarse-grained systems, such as nucleic acid secondary structure, is advantageous for being able to access behavior at long time scales, even minutes or hours. Transition rates between coarse-grained states depend upon intermediate barriers, which are not directly simulated. W ... [Phys. Rev. E 84, 061912 ] published .

The unfolded protein response supports cellular robustness as a broad-spectrum compensatory pathway

Guillaume Thibault, Nurzian Ismail, and Davis T. W. Ng
Stress pathways monitor intracellular systems and deploy a range of regulatory mechanisms in response to stress. One of the best-characterized pathways, the unfolded protein response (UPR), is responsible for maintaining endoplasmic reticulum (ER) homeostasis. The highly conserved Ire1 branch regul ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20597 (2011)] published Thu Dec 22, 2011.

Retraction for Dougan et al., Solvent molecules bridge the mechanical unfolding transition state of a protein

Abstract not available. [Proc. Natl. Acad. Sci. U.S.A. 108, 20850 (2011)] published Thu Dec 22, 2011.

GlcNAcylation of histone H2B facilitates its monoubiquitination

Ryoji Fujiki, Waka Hashiba, Hiroki Sekine, Atsushi Yokoyama, Toshihiro Chikanishi et al.
Chromatin reorganization is governed by multiple post-translational modifications of chromosomal proteins and DNA. These histone modifications are reversible, dynamic events that can regulate DNA-driven cellular processes. However, the molecular mechanisms that coordinate histone modification patte ... [Nature 480, 557 (2011)] published Thu Dec 22, 2011.

The Ribosome Modulates Nascent Protein Folding

Christian M. Kaiser, Daniel H. Goldman, John D. Chodera, Ignacio Tinoco, Jr., and Carlos Bustamante
Proteins are synthesized by the ribosome and generally must fold to become functionally active. Although it is commonly assumed that the ribosome affects the folding process, this idea has been extremely difficult to demonstrate. We have developed an experimental system to investigate the folding of ... [Science 334, 1723 (2011)] published Thu Dec 22, 2011.

Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser

Lukas Lomb, Thomas R. M. Barends, Stephan Kassemeyer, Andrew Aquila, Sascha W. Epp et al.
X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV pho ... [Phys. Rev. B 84, 214111 ] published .

Modeling of relay helix functional dynamics and feasibility of experimental verification by neutron scattering

Miljko V. Sataric, Slobodan Zdravkovic, and Jack A. Tuszynski
Cellular long-range transport involves motor proteins (MPs) (especially, kinesin and myosin) which contain a so-called relay helix. Its motion is of crucial importance to the conversion of chemical energy released in ATP hydrolysis into the coordinated mechanical movement of the entire motor protein ... [Chaos 21, 043135 (2011)] published Thu Dec 22, 2011.

Preferential solvation of lysozyme in water/ethanol mixtures

Maria Grazia Ortore, Paolo Mariani, Flavio Carsughi, Stefania Cinelli, Giuseppe Onori et al.
We provide a quantitative description of the solvation properties of lysozyme in water/ethanol mixtures, which has been obtained by a simultaneous analysis of small-angle neutron scattering and differential scanning calorimetry experiments. All data sets were analyzed by an original method, which in ... [J. Chem. Phys. 135, 245103 (2011)] published Fri Dec 23, 2011.

Transition network based on equilibrium sampling: A new method for extracting kinetic information from Monte Carlo simulations of protein folding

Konstantin V. Klenin and Wolfgang Wenzel
We propose a new type of transition network for modeling of protein dynamics. The nodes of the network correspond to the conformations taken from random sampling of equilibrium ensemble available, e.g., by Monte Carlo simulations. Although this approach does not provide absolute values of folding/un ... [J. Chem. Phys. 135, 235105 (2011)] published Wed Dec 21, 2011.

Experimental free energy surfaces reveal the mechanisms of maintenance of protein solubility

Alfonso De Simone, Anne Dhulesia, Gemma Soldi, Michele Vendruscolo, Shang-Te Danny Hsu et al.
The identification of the factors that enable normally folded proteins to remain in their soluble and functional states is crucial for a comprehensive understanding of any biological system. We have determined a series of energy landscapes of the acylphosphatase from Drosophila melanogaster under a ... [Proc. Natl. Acad. Sci. U.S.A. 108, 21057 (2011)] published Thu Dec 29, 2011.

Protein conformational dynamics in the mechanism of HIV-1 protease catalysis

Vladimir Yu. Torbeev, H. Raghuraman, Donald Hamelberg, Marco Tonelli, William M. Westler et al.
We have used chemical protein synthesis and advanced physical methods to probe dynamics-function correlations for the HIV-1 protease, an enzyme that has received considerable attention as a target for the treatment of AIDS. Chemical synthesis was used to prepare a series of unique analogues of the ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20982 (2011)] published Thu Dec 29, 2011.

Protein dynamical transition at 110 K

Chae Un Kim, Mark W. Tate, and Sol M. Gruner
Proteins are known to undergo a dynamical transition at around 200 K but the underlying mechanism, physical origin, and relationship to water are controversial. Here we report an observation of a protein dynamical transition as low as 110 K. This unexpected protein dynamical transition precisely co ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20897 (2011)] published Thu Dec 29, 2011.

Multiple molecular architectures of the eye lens chaperone alphaB-crystallin elucidated by a triple hybrid approach

Nathalie Braun, Martin Zacharias, Jirka Peschek, Andreas Kastenmuller, Juan Zou et al.
The molecular chaperone alphaB-crystallin, the major player in maintaining the transparency of the eye lens, prevents stress-damaged and aging lens proteins from aggregation. In nonlenticular cells, it is involved in various neurological diseases, diabetes, and cancer. Given its structural plastici ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20491 (2011)] published Thu Dec 22, 2011.

Structure change of beta-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study

Qiang Shao, Lijiang Yang, and Yi Qin Gao
Our previous study showed that for the tested polypeptides which have similar beta-hairpin structures but different sequences, their folding free energy pathways are dominantly determined by the turn conformational propensity. In this study, we study how the turn conformational propensity affects th ... [J. Chem. Phys. 135, 235104 (2011)] published Tue Dec 20, 2011.

Denaturation of proteins near polar surfaces

Anna Starzyk and Marek Cieplak
All-atom molecular dynamics simulations for proteins placed near a model mica surface indicate existence of two types of evolution. One type leads to the surface-induced unfolding and the other just to a deformation. The two behaviors are characterized by distinct properties of the radius of gyratio ... [J. Chem. Phys. 135, 235103 (2011)] published Tue Dec 20, 2011.

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

Santanu Roy, Joshua Lessing, Georg Meisl, Ziad Ganim, Andrei Tokmakoff et al.
We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are n ... [J. Chem. Phys. 135, 234507 (2011)] published Mon Dec 19, 2011.

RNAprotein binding interface in the telomerase ribonucleoprotein

Christopher J. Bley, Xiaodong Qi, Dustin P. Rand, Chad R. Borges, Randall W. Nelson et al.
Telomerase is a specialized reverse transcriptase containing an intrinsic telomerase RNA (TR) which provides the template for telomeric DNA synthesis. Distinct from conventional reverse transcriptases, telomerase has evolved a unique TR-binding domain (TRBD) in the catalytic telomerase reverse tran ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20333 (2011)] published Thu Dec 22, 2011.

Universal geometrical factor of protein conformations as a consequence of energy minimization

Ming-Chya Wu, Mai Li, Wen-Jong Ma, Maksim Kouza, and Chin-Kun Hu
The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein conformation as a consequence of energy minimization in protein fo ... [EPL 96, 68005 (2011)] published Thu Dec 22, 2011.

Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket

Ryosuke Nakashima, Keisuke Sakurai, Seiji Yamasaki, Kunihiko Nishino, and Akihito Yamaguchi
AcrB and its homologues are the principal multidrug transporters in Gram-negative bacteria and are important in antibiotic drug tolerance. AcrB is a homotrimer that acts as a tripartite complex with the outer membrane channel TolC and the membrane fusion protein AcrA. Minocycline and doxorubicin ha ... [Nature 480, 565 (2011)] published Thu Dec 22, 2011.

Percolation, phase separation, and gelation in fluids and mixtures of spheres and rods

Ryan Jadrich and Kenneth S. Schweizer
The relationship between kinetic arrest, connectivity percolation, structure and phase separation in protein, nanoparticle, and colloidal suspensions is a rich and complex problem. Using a combination of integral equation theory, connectivity percolation methods, naive mode coupling theory, and the ... [J. Chem. Phys. 135, 234902 (2011)] published Wed Dec 21, 2011.

Four-dimensional structural dynamics of sheared collagen networks

Richard C. Arevalo, Jeffrey S. Urbach, and Daniel L. Blair
Abstract not available. [Chaos 21, 041102 (2011)] published Tue Dec 20, 2011.

Effects of chain stiffness and salt concentration on responses of polyelectrolyte brushes under external electric field

Qianqian Cao, Chuncheng Zuo, Lujuan Li, and Guang Yan
We report a molecular dynamics study on non-equilibrium dynamics of polyelectrolyte brushes under external electric fields. In this work, the effects of chain stiffness and salt concentration on static and dynamic responses of the brushes are addressed in detail. Our simulations indicate that varyin ... [Biomicrofluidics 5, 044119 (2011)] published Wed Dec 21, 2011.

First-principles simulations of exciton diffusion in organic semiconductors

Xu Zhang, Zi Li, and Gang Lu
Exciton diffusion is crucial for the performance of organic semiconductors in photovoltaic and solid state lighting applications. We propose a first-principles approach that can predict exciton dynamics in organic semiconductors. The method is based on time-dependent density functional theory to des ... [Phys. Rev. B 84, 235208 ] published .

Free energy of alternating two-component polymer brushes on cylindrical templates

William L. Miller, Behnaz Bozorgui, Katherine Klymko, and Angelo Cacciuto
We use computer simulations to investigate the stability of a two-component polymer brush de-mixing on a curved template into phases of different morphological properties. It has been previously shown via molecular dynamics simulations that immiscible chains having different length and anchored to a ... [J. Chem. Phys. 135, 244902 (2011)] published Tue Dec 27, 2011.

Free Energy of Multiple Overlapping Chains

Katherine Klymko and Angelo Cacciuto
How accurate is pair additivity in describing interactions between soft polymer-based nanoparticles? Using numerical simulations we compute the free energy cost required to overlap multiple chains in the same region of space, and provide a quantitative measure of the effectiveness of pair additivity ... [Phys. Rev. Lett. 107, 278302 ] published .

Adsorption and self-assembly of biosurfactants studied by neutron reflectivity and small angle neutron scattering: glycolipids, lipopeptides and proteins

Jeffrey Penfold, Robert K Thomas, and Hsin-Hui Shen
Biosurfactants are surface active biomolecules that are produced by a variety of different micro-organisms. The current environmental requirements for more biosustainable, biocompatible and biodegradable surfactant based products make the study of biosurfactants an important area of research. Unders ... [Soft Matter 8, 578 (2011)] published Fri Dec 16, 2011.

Perforin activity at membranes leads to invaginations and vesicle formation

Tilen Praper, Andreas F.-P. Sonnen, Ales Kladnik, Alberto O. Andrighetti, Gabriella Viero et al.
The cytotoxic cell granule secretory pathway is essential for immune defence. How the pore-forming protein perforin (PFN) facilitates the cytosolic delivery of granule-associated proteases (granzymes) remains enigmatic. Here we show that PFN is able to induce invaginations and formation of complete ... [Proc. Natl. Acad. Sci. U.S.A. 108, 21016 (2011)] published Thu Dec 29, 2011.

Characterization of cholesterol-depleted or -restored cell membranes by depth-sensing nano-indentation

Yun-Ta Yang, Jiunn-Der Liao, Chou-Ching K. Lin, Cheng-Tao Chang, Shyh-Hau Wang et al.
Cholesterol is a major component of eukaryotic cell membranes. It is well-accepted that cholesterol depletion triggers a complicated cascade of biochemical reactions which may affect many cell processes. However, the effect of cholesterol depletion on the deformability of cell membranes is still con ... [Soft Matter 8, 682 (2011)] published Fri Dec 16, 2011.

Computer simulations of fusion, fission and shape deformation in lipid membranes

Kai Yang and Yu-qiang Ma
Fusion and fission are two kinds of crucial cellular activities related to cell membranes. Therefore, the studies on fusion and fission are particularly important for the understanding of the nature of cell membranes. In this review, the recent studies on fusion, fission and shape deformation in the ... [Soft Matter 8, 606 (2011)] published Fri Dec 16, 2011.

Membrane mediated regulation in free peptides of HIV-1 gp41: minimal modulation of the hemifusion phase

Eleonora Cerasoli, Jascindra Ravi, Craig Gregor, Rohanah Hussain, Giuliano Siligardi et al.
Membrane-mediated structural modulation in two short fragments of the human HIV-1 envelope protein gp41 is demonstrated. Derived from the C-terminal membrane proximal external (MPE) and N-terminal fusion peptide proximal (FPP) regions, these peptides are widely separated in the primary sequence but ... [Phys. Chem. Chem. Phys. 14, 1277 (2011)] published Fri Dec 16, 2011.

Thermal fluctuations in shape, thickness, and molecular orientation in lipid bilayers

Max C. Watson, Evgeni S. Penev, Paul M. Welch, and Frank L. H. Brown
We present a unified continuum-level model for bilayer energetics that includes the effects of bending, compression, lipid orientation (tilting relative to the monolayer surface normal), and microscopic noise (protrusions). Expressions for thermal fluctuation amplitudes of several physical quantitie ... [J. Chem. Phys. 135, 244701 (2011)] published Thu Dec 22, 2011.

Gating of the MlotiK1 potassium channel involves large rearrangements of the cyclic nucleotide-binding domains

Stefania A. Mari, Joao Pessoa, Stephen Altieri, Ulf Hensen, Lise Thomas et al.
Cyclic nucleotide-regulated ion channels are present in bacteria, plants, vertebrates, and humans. In higher organisms, they are closely involved in signaling networks of vision and olfaction. Binding of cAMP or cGMP favors the activation of these ion channels. Despite a wealth of structural and st ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20802 (2011)] published Thu Dec 22, 2011.

Alternatively spliced domains interact to regulate BK potassium channel gating

Brandon E. Johnson, Dominique A. Glauser, Elise S. Dan-Glauser, D. Brent Halling, Richard W. Aldrich et al.
Most human genes contain multiple alternative splice sites believed to extend the complexity and diversity of the proteome. However, little is known about how interactions among alternative exons regulate protein function. We used the Caenorhabditis elegans slo-1 large-conductance calcium and volta ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20784 (2011)] published Thu Dec 22, 2011.

Curvature multiphase field model for phase separation on a membrane

C. Varea, R. A. Barrio, and A. Hernandez-Machado
We propose a model to describe the physical mechanisms by which chemical substances separate in the vicinity of a membrane. We assume that the adsorption of the different components of a complex liquid on a membrane is governed by interactions that couple them to the spontaneous curvature of the mem ... [Phys. Rev. E 84, 061922 ] published .

Boundary-induced orientation of dynamic filament networks and vesicle agglomerations

Philip Greulich and Ludger Santen
We find a statistical mechanism that can adjust orientations of intracellular filaments to cell geometry in the absence of organizing centers. The effect is based on random and isotropic filament (de-)polymerization dynamics and is independent of filament interactions and explicit regulation. It can ... [Phys. Rev. E 84, 060902 ] published .

Hydrogen-bonded multilayers of micelles of a dually responsive dicationic block copolymer

Irem Erel, H. Enis Karahan, Cansel Tuncer, Vural Butun, and A. Levent Demirel
We report the fabrication of hydrogen-bonded multilayers of micelles of a dually responsive, dicationic block copolymer, poly[2-(N-morpholino)ethyl methacrylate-block-2-(diisopropylamino)ethyl methacrylate] (PMEMA-b-PDPA). By taking advantage of the difference in the hydrophilicity of PMEMA and PDPA ... [Soft Matter 8, 827 (2011)] published Fri Dec 16, 2011.

Energy relaxation of intermolecular motions in supercooled water and ice: A molecular dynamics study

Takuma Yagasaki and Shinji Saito
We investigate the energy relaxation of intermolecular motions in liquid water at temperatures ranging from 220 K to 300 K and in ice at 220 K using molecular dynamics simulations. We employ the recently developed frequency resolved transient kinetic energy analysis, which provides detailed informat ... [J. Chem. Phys. 135, 244511 (2011)] published Thu Dec 29, 2011.

Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. II. Canonical and isokinetic ensembles

Igor P. Omelyan and Andriy Kovalenko
We have developed several multiple time stepping techniques to overcome the limitations on efficiency of molecular dynamics simulations of complex fluids. They include the modified canonical and isokinetic schemes, as well as the extended isokinetic Nose-Hoover chain approach. The latter generalizes ... [J. Chem. Phys. 135, 234107 (2011)] published Mon Dec 19, 2011.

A molecular dynamics study of water nucleation using the TIP4P/2005 model

Alejandro Perez and Angel Rubio
Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. ... [J. Chem. Phys. 135, 244505 (2011)] published Thu Dec 29, 2011.

On a relationship between molecular polarizability and partial molar volume in water

Ekaterina L. Ratkova and Maxim V. Fedorov
We reveal a universal relationship between molecular polarizability (a single-molecule property) and partial molar volume in water that is an ensemble property characterizing solute-solvent systems. Since both of these quantities are of the key importance to describe solvation behavior of dissolved ... [J. Chem. Phys. 135, 244109 (2011)] published Fri Dec 30, 2011.

Computing the energy of a water molecule using multideterminants: A simple, efficient algorithm

Bryan K. Clark, Miguel A. Morales, Jeremy McMinis, Jeongnim Kim, and Gustavo E. Scuseria
Quantum Monte Carlo (QMC) methods such as variational Monte Carlo and fixed node diffusion Monte Carlo depend heavily on the quality of the trial wave function. Although Slater-Jastrow wave functions are the most commonly used variational ansatz in electronic structure, more sophisticated wave funct ... [J. Chem. Phys. 135, 244105 (2011)] published Tue Dec 27, 2011.

Increase of both Order and Disorder in the First Hydration Shell with Increasing Solute Polarity

Aljaz Godec, Jeremy C. Smith, and Franci Merzel
Monte Carlo simulations of a small model solute in an aqueous solution are used to examine the effects of solute polarity on hydration structure. A judicious definition of the orientational order parameter leads to reinterpretation of the conventional picture of hydration. As the solute varies from ... [Phys. Rev. Lett. 107, 267801 ] published .

Conformational fluctuations of a proteinDNA complex and the structure and ordering of water around it

Sudipta Kumar Sinha and Sanjoy Bandyopadhyay
ProteinDNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expe ... [J. Chem. Phys. 135, 245104 (2011)] published Fri Dec 23, 2011.

A two-dimensional-reference interaction site model theory for solvation structure near solid-liquid interface

Kenji Iida and Hirofumi Sato
We develop a new equation to describe solvation structure near solid-liquid interface at the atomic-level. The developed equation focuses on anisotropy of solvation structure near the interface by using two-dimensional density distribution of solvent along two directions, one of which is perpendicul ... [J. Chem. Phys. 135, 244702 (2011)] published Thu Dec 22, 2011.

Direct evidence of quantum transport in photosynthetic light-harvesting complexes

Gitt Panitchayangkoon, Dmitri V. Voronine, Darius Abramavicius, Justin R. Caram, Nicholas H. C. Lewis et al.
The photosynthetic light-harvesting apparatus moves energy from absorbed photons to the reaction center with remarkable quantum efficiency. Recently, long-lived quantum coherence has been proposed to influence efficiency and robustness of photosynthetic energy transfer in light-harvesting antennae. ... [Proc. Natl. Acad. Sci. U.S.A. 108, 20908 (2011)] published Thu Dec 29, 2011.

Color modeling of protein optical probes

N. Arul Murugan, Jacob Kongsted, Zilvinas Rinkevicius, and Hans Agren
We present a strategy for modeling optical probes within heterogeneous environments of restricted dimension. The method is based on a multiphysics approach comprising sequential structure modeling by means of hybrid CarParrinello molecular dynamics and property modeling by means of quantum mechanics ... [Phys. Chem. Chem. Phys. 14, 1107 (2011)] published Fri Dec 16, 2011.

Communication: Quantum polarized fluctuating charge model: A practical method to include ligand polarizability in biomolecular simulations

S. Roy Kimura, Ramkumar Rajamani, and David R. Langley
We present a simple and practical method to include ligand electronic polarization in molecular dynamics (MD) simulation of biomolecular systems. The method involves periodically spawning quantum mechanical (QM) electrostatic potential (ESP) calculations on an extra set of computer processors using ... [J. Chem. Phys. 135, 231101 (2011)] published Wed Dec 21, 2011.

Cancer immunotherapy comes of age

Ira Mellman, George Coukos, and Glenn Dranoff
Activating the immune system for therapeutic benefit in cancer has long been a goal in immunology and oncology. After decades of disappointment, the tide has finally changed due to the success of recent proof-of-concept clinical trials. Most notable has been the ability of the anti-CTLA4 antibody, ... [Nature 480, 480 (2011)] published Thu Dec 22, 2011.