The influence of direct motor-motor interaction in models for cargo transport by a single team of motors.

abstract：:The Q-cycle mechanism plays an important role in the conversion of the redox energy into the energy of the proton electrochemical gradient across the biomembrane. The bifurcated electron transfer reaction, which is built into this mechanism, recycles one electron, thus allowing us to translocate two protons per one el...

journal_title：Physical biology

authors： Smirnov AY,Nori F

更新日期：2012-02-01 00:00:00

abstract：:Bistable regulatory elements enhance heterogeneity in cell populations and, in multicellular organisms, allow cells to specialize and specify their fate. Our study demonstrates that in a system of bistable genetic switch, the noise characteristics control in which of the two epigenetic attractors the cell population w...

journal_title：Physical biology

authors： Jaruszewicz J,Lipniacki T

更新日期：2013-06-01 00:00:00

abstract：:Several viruses exploit clathrin-mediated endocytosis to gain entry into host cells. This process is also used extensively in biomedical applications to deliver nanoparticles (NPs) to diseased cells. The internalization of these nano-objects is controlled by the assembly of a clathrin-containing protein coat on the cy...

journal_title：Physical biology

authors： Banerjee A,Berezhkovskii A,Nossal R

更新日期：2016-02-12 00:00:00

abstract：:Oscillations play an important physiological role in a variety of biological systems. For example, respiration and carbohydrate synthesis are coupled to the circadian clock in cyanobacteria (Ishiura et al 1998 Science 281 1519) and ultradian oscillations with time periods of a few hours have been observed in immune re...

journal_title：Physical biology

authors： Krishna S,Semsey S,Jensen MH

更新日期：2009-05-21 00:00:00

abstract：:When the author arrived in Berkeley, in the mid 1970s, to study Biophysics he soon felt as if he was engaging himself in a somewhat marginal activity. Biology was then entering another of its cyclical periods of annotation that was to culminate with the human genome project. Two decades later, however, at the end of t...

journal_title：Physical biology

authors： Bustamante CJ

更新日期：2014-10-08 00:00:00

abstract：:Particle-based simulators represent molecules of interest with point-like particles that diffuse and react in continuous space. These simulators are often used to investigate spatial or stochastic aspects of biochemical systems. This paper presents new particle-based simulation algorithms for modeling interactions bet...

journal_title：Physical biology

authors： Andrews SS

更新日期：2009-11-12 00:00:00

abstract：:Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts within households and more distant contacts between the households. The epidemic transmission dynamics is significantly modified as a consequence. W...

journal_title：Physical biology

authors： Huber G,Kamb M,Kawagoe K,Li LM,Veytsman B,Yllanes D,Zigmond D

更新日期：2020-10-21 00:00:00

abstract：:Directed cell migration often involves at least two types of cell motility that include multicellular streaming and chain migration. However, what is unclear is how cell contact dynamics and the distinct microenvironments through which cells travel influence the selection of one migratory mode or the other. The embryo...

journal_title：Physical biology

authors： Wynn ML,Rupp P,Trainor PA,Schnell S,Kulesa PM

更新日期：2013-06-01 00:00:00

abstract：:We carry out systematic Monte Carlo simulations of Gō lattice proteins to investigate and compare the folding processes of two model proteins whose native structures differ from each other due to the presence of a trefoil knot located near the terminus of one of the protein chains. We show that the folding time of the...

journal_title：Physical biology

authors： Faísca PF,Travasso RD,Charters T,Nunes A,Cieplak M

更新日期：2010-02-03 00:00:00

abstract：:Thrombosis accounts for 80% of deaths in patients with diabetes mellitus. Diabetic patients demonstrate tortuous microvessels and larger than normal platelets. Large platelets are associated with increased platelet activation and thrombosis, but the physical effects of large platelets in the microscale processes of th...

journal_title：Physical biology

authors： Chesnutt JK,Han HC

更新日期：2013-10-01 00:00:00

abstract：:A cluster of neural crest cells (NCCs) may chemotax up a shallow external gradient to which a single cell is unresponsive. To explain this intriguing 'group advantage', we propose a chemo-mechanical model based on the signaling proteins Rac1 and RhoA. We represent each cell as a polygon with nodes connected by elastic...

journal_title：Physical biology

authors： Merchant B,Feng JJ

更新日期：2020-03-10 00:00:00

abstract：:Tissue factor (TF) is a transmembrane glycoprotein cofactor of activated blood coagulation factor VII (FVIIa) that is required for hemostatic thrombin generation at sites of blood vessel injury. Membrane-associated TF detected in circulating blood of healthy subjects, referred to as intravascular or circulating TF has...

journal_title：Physical biology

authors： Tormoen GW,Rugonyi S,Gruber A,McCarty OJ

更新日期：2011-12-01 00:00:00

abstract：:We propose a three-dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue plasticity is modeled by a stochastic process consisting of a connectivity change (addi...

journal_title：Physical biology

authors： Czirok A,Isai DG

更新日期：2014-12-15 00:00:00

abstract：:Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation diagram and characterize the bistable and the monostable regimes. The main focus of...

journal_title：Physical biology

authors： Dayarian A,Sengupta AM

更新日期：2013-06-01 00:00:00

abstract：:'ENVIRONMENT' is a computational platform that has been developed in the last few years with the aim to simulate stochastically the dynamics and stability of chemically reacting protocellular systems. Here we present and describe some of its main features, showing how the stochastic kinetics approach can be applied to...

journal_title：Physical biology

authors： Mavelli F,Ruiz-Mirazo K

更新日期：2010-08-11 00:00:00

abstract：:Bacteria such as Escherichia coli propel themselves by rotating a bundle of helical filaments, each driven by a rotary motor embedded in the cell membrane. Each filament is an assembly of thousands of copies of the protein flagellin which assumes two different states. We model the filament by an elastic network of rig...

journal_title：Physical biology

authors： Speier C,Vogel R,Stark H

更新日期：2011-08-01 00:00:00

abstract：:The single-molecule fluorescence technique is becoming a general and mature tool to probe interactions and dynamics of biomolecules with ultra high precision and accuracy. However, nonspecific adsorption of biomolecules to the flow cells remains a major experimental riddle for the study of many complex biological syst...

journal_title：Physical biology

authors： Pan H,Xia Y,Qin M,Cao Y,Wang W

更新日期：2015-06-29 00:00:00

abstract：:Engineering artificial cells to mimic one or multiple fundamental cell biological functions is an emerging area of synthetic biology. Reconstituting functional modules from biological components in vitro is a challenging yet an important essence of bottom-up synthetic biology. Here we describe the concept of building ...

journal_title：Physical biology

authors： Majumder S,Liu AP

更新日期：2017-12-06 00:00:00

abstract：:The DFT:B3LYP (6-31G** basis set) method, including the hyperfine and spin-orbit couplings (HFC and SOC, respectively), is used to study the separation of two complementary trinucleotide sequences, (dC-dG-dA)-(dG-dC-dT), upon the action of two Mg(2+) cofactors (a simplified model). The computations reveal a crossing o...

journal_title：Physical biology

authors： Tulub AA,Stefanov VE

更新日期：2015-12-10 00:00:00

abstract：:Epithelial-to-mesenchymal transition (EMT) is a fundamental developmental process wherein polarized epithelial cells lose their junctional architecture and apical-basal polarity to become motile mesenchymal cells, and there is emerging evidence for its role in propagating tumor dissemination. While many multifaceted n...

journal_title：Physical biology

authors： Antony J,Thiery JP,Huang RY

更新日期：2019-05-07 00:00:00

abstract：:The tripartite synapse denotes the junction of a pre- and postsynaptic neuron modulated by a synaptic astrocyte. Enhanced transmission probability and frequency of the postsynaptic current-events are among the significant effects of the astrocyte on the synapse as experimentally characterized by several groups. In thi...

journal_title：Physical biology

authors： Nadkarni S,Jung P

更新日期：2007-01-09 00:00:00

abstract：:Gene expression is an intrinsically noisy process, typically, producing mRNAs and proteins in bursts. An important description of such stochastic processes can be done in terms of the mean first passage time (MFPT), i.e., the time taken by mRNAs/proteins to reach a particular threshold. We study the role of burstiness...

journal_title：Physical biology

authors： Shreshtha M,Surendran A,Ghosh A

更新日期：2016-05-20 00:00:00

abstract：:A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication o...

journal_title：Physical biology

authors： Rapaport DC

更新日期：2010-12-09 00:00:00

abstract：:We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMs). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structures, assuming we know the native fold. ...

journal_title：Physical biology

authors： Thomas S,Song G,Amato NM

更新日期：2005-11-09 00:00:00

abstract：:Transendothelial migration is a crucial process of the metastatic cascade in which a malignant cell attaches itself to the endothelial layer forming the inner wall of a blood or lymph vessel and creates a gap through which it enters into the bloodstream (or lymphatic system) and then is transported to distant parts of...

journal_title：Physical biology

authors： Ramis-Conde I,Chaplain MA,Anderson AR,Drasdo D

更新日期：2009-03-25 00:00:00

abstract：:Successful biological development via spatial regulation of cell differentiation relies on the action of multiple signaling molecules that are known as morphogens. It is now well-established that signaling molecules create non-uniform concentration profiles, morphogen gradients, that activate different genes, leading ...

journal_title：Physical biology

authors： Teimouri H,Kolomeisky AB

更新日期：2015-04-17 00:00:00

abstract：:Motile biological cells in tissue often display the phenomenon of durotaxis, i.e. they tend to move towards stiffer parts of substrate tissue. The mechanism for this behavior is not completely understood. We consider simplified models for durotaxis based on the classic persistent random walker scheme. We show that eve...

journal_title：Physical biology

authors： Doering CR,Mao X,Sander LM

更新日期：2018-09-11 00:00:00

abstract：:Growing evidence suggests that critical cellular processes are profoundly influenced by the cross talk between extracellular nanomechanical forces and the material properties of the cellular microenvironment. Although many studies have examined either the effect of nanomechanical forces or the material properties of t...

journal_title：Physical biology

authors： Al-Rekabi Z,Pelling AE

更新日期：2013-12-01 00:00:00

abstract：:Cells moving on a two dimensional substrate generate motion by polymerizing actin filament networks inside a flat membrane protrusion. New filaments are generated by branching off existing ones, giving rise to branched network structures. We investigate the force-extension relation of branched filaments, grafted on an...

journal_title：Physical biology

authors： Razbin M,Falcke M,Benetatos P,Zippelius A

更新日期：2015-06-04 00:00:00

abstract：:This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle-field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale sy...

journal_title：Physical biology

authors： Milano G,Kawakatsu T,De Nicola A

更新日期：2013-08-01 00:00:00