Modeling the Q-cycle mechanism of transmembrane energy conversion.

abstract：:Cell signaling is achieved predominantly by reversible phosphorylation-dephosphorylation reaction cascades. Up until now, circuits conferring adaptation have all required the presence of a cascade with some type of closed topology: negative-feedback loop with a buffering node, or incoherent feed-forward loop with a pr...

journal_title：Physical biology

authors： Srividhya J,Li Y,Pomerening JR

更新日期：2011-08-01 00:00:00

abstract：:In the intracellular environment, the intrinsic dynamics of microtubule filaments is often hindered by the presence of barriers of various kind, such as kinetochore complexes and cell cortex, which impact their polymerisation force and dynamical properties such as catastrophe rate. We present a theoretical study of th...

journal_title：Physical biology

authors： Yadav V,Srinivas B,Gopalakrishnan M

更新日期：2020-10-12 00:00:00

abstract：:Type I collagen is a versatile biomaterial that is widely used in medical applications due to its weak antigenicity, robust biocompatibility, and its ability to be modified for a wide array of applications. As such, collagen has become a major component of many tissue engineering scaffolds, drug delivery platforms, an...

journal_title：Physical biology

authors： Hapach LA,VanderBurgh JA,Miller JP,Reinhart-King CA

更新日期：2015-12-21 00:00:00

abstract：:The Golgi apparatus has intrigued researchers since its discovery and despite the advances, there are still many open questions in regards to its shape and function. We propose a mechanical model of Golgi apparatus stack and explain its most elementary geometrical properties: the equilibrium number of cisternae, the s...

journal_title：Physical biology

authors： Jelerčič U

更新日期：2019-09-05 00:00:00

abstract：:Traditionally animal groups have been characterized by the macroscopic patterns that they form. It is now recognised that such patterns convey limited information about the nature of the aggregation as a whole. Aggregate properties cannot be determined by passive observations alone; instead one must interact with them...

journal_title：Physical biology

authors： Reynolds AM

更新日期：2019-04-23 00:00:00

abstract：:Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevol...

journal_title：Physical biology

authors： Mukherjee S,Weimer KE,Seok SC,Ray WC,Jayaprakash C,Vieland VJ,Swords WE,Das J

更新日期：2014-12-04 00:00:00

abstract：:Modeling the spatiotemporal dynamics of biochemical reaction systems at single-molecule resolution has become feasible with the increase of computing power and is applied especially to cellular signal transduction. For an association reaction the two molecules have to be in contact. Hence, a physically faithful model ...

journal_title：Physical biology

authors： Klann M,Koeppl H

更新日期：2013-08-01 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：:The maintenance of tissue integrity is essential for the life of multicellular organisms. Healing of a skin wound is a paradigm for how various cell types localize and repair tissue perturbations in an orchestrated fashion. To investigate biophysical mechanisms associated with wound localization, we focus on a model s...

journal_title：Physical biology

authors： Lembong J,Sabass B,Stone HA

更新日期：2017-06-28 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：:Sequence-dependent DNA flexibility is an important structural property originating from the DNA 3D structure. In this paper, we investigate the DNA flexibility of the budding yeast (S. Cerevisiae) replication origins on a genome-wide scale using flexibility parameters from two different models, the trinucleotide and t...

journal_title：Physical biology

authors： Cao XQ,Zeng J,Yan H

更新日期：2008-09-29 00:00:00

abstract：:This comment argues against the view that cancer cells produce less entropy than normal cells as stated in a recent paper by Marín and Sabater. The basic principle of estimation of entropy production rate in a living cell is discussed, emphasizing the fact that entropy production depends on both the amount of heat exc...

journal_title：Physical biology

authors： Sadeghi Ghuchani M

更新日期：2018-02-08 00:00:00

abstract：:This paper considers the generation of trajectories to a given protein conformation and presents a novel approach based on artificial potential functions--originally proposed for multi-robot navigation. The artificial potential function corresponds to a simplified energy model, but with the novelty that--motivated by ...

journal_title：Physical biology

authors： Ulutaş B,Haliloglu T,Bozma I

更新日期：2009-05-14 00:00:00

abstract：:The detection of gravity plays a fundamental role during the growth and evolution of plants. Although progress has been made in our understanding of the molecular, cellular and physical mechanisms involved in the gravity detection, a coherent scenario consistent with all the observations is still lacking. In this spec...

journal_title：Physical biology

authors： Pouliquen O,Forterre Y,Bérut A,Chauvet H,Bizet F,Legué V,Moulia B

更新日期：2017-05-23 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：:Based on the experimental evidence that translating ribosomes stabilize the mRNAs, we introduce and study a theoretical model for the dynamic shielding of mRNA by ribosomes. We present an improved fitting of published decay assay data in E. coli and show that only one third of the decay patterns are exponential. Our n...

journal_title：Physical biology

authors： Deneke C,Lipowsky R,Valleriani A

更新日期：2013-08-01 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：:Tumor metastasis involves a progressive loss of tissue architecture and dissolution of structural boundaries between the epithelium and connective tissue. The basement membrane (BM), a specialized network of extracellular matrix proteins forms a barrier that physically restricts pre-invasive lesions such that they rem...

journal_title：Physical biology

authors： Tanner K

更新日期：2012-12-01 00:00:00

abstract：:Cellular networks have been the focus of studies in modern systems biology. They are crucial in understanding cell functions and related diseases. We review some past progress in both the theory and experiments, and we also provide several future perspectives for the field. ...

journal_title：Physical biology

authors： Fang X,Wang J

更新日期：2017-02-16 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：:Single-molecule manipulation has allowed the forced unfolding of multidomain proteins. Here we develop a theory that not only explains these experiments, but also points out a number of difficulties in their interpretation and makes suggestions for further experiments. Our theory is valid for essentially any molecule ...

journal_title：Physical biology

authors： Staple DB,Payne SH,Reddin AL,Kreuzer HJ

更新日期：2009-07-01 00:00:00

abstract：:Calcium homeostasis is considered to be one of the most important factors for the contraction and relaxation of the heart muscle. However, under some pathological conditions, such as heart failure (HF), calcium homeostasis is disordered, and spontaneous waves may occur. In this study, we developed a mathematical model...

journal_title：Physical biology

authors： Lu L,Xia L,Ye X,Cheng H

更新日期：2010-05-26 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：:How interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image an...

journal_title：Physical biology

authors： Lenne PF,Munro E,Heemskerk I,Warmflash A,Bocanegra-Moreno L,Kishi K,Kicheva A,Long Y,Fruleux A,Boudaoud A,Saunders TE,Caldarelli P,Michaut A,Gros J,Maroudas-Sacks Y,Keren K,Hannezo E,Gartner ZJ,Stormo BS,Gladfelter

更新日期：2020-12-04 00:00:00

abstract：:The important role of cation-chloride co-transporters in epilepsy is being supported by an increasing number of investigations. However, enormous complexity is involved since the action of these co-transporters has effects on the ionic homeostasis influencing directly the neuronal excitability and the tissue propensit...

journal_title：Physical biology

authors： Lopes MR,Santos LE,Rodrigues AM,Duarte MA,Infantosi AF,Scorza FA,Arida RM,Madureira AP,da Silveira GA,dos Santos IC,Cavalheiro EA,de Almeida AC

更新日期：2013-10-01 00:00:00

abstract：:The asymmetric cell division cycle in Caulobacter crescentus is controlled by an elaborate molecular mechanism governing the production, activation and spatial localization of a host of interacting proteins. In previous work, we proposed a deterministic mathematical model for the spatiotemporal dynamics of six major r...

journal_title：Physical biology

authors： Li F,Subramanian K,Chen M,Tyson JJ,Cao Y

更新日期：2016-06-25 00:00:00

abstract：:To address the issue of extracting useful information from large data-set of large scale networks of neurons, we propose an algorithm that involves both algebraic-statistical and topological tools. We investigate the electrical behavior of in vitro cortical assemblies both during spontaneous and stimulus-evoked activi...

journal_title：Physical biology

authors： Pirino V,Riccomagno E,Martinoia S,Massobrio P

更新日期：2015-01-05 00:00:00

abstract：:Self-organization processes in multicellular aggregates of bacteria and amoebae offer fascinating insights into the evolution of cooperation and differentiation of cells. During myxobacterial development a variety of spatio-temporal patterns emerges such as counterpropagating waves of cell density that are known as ri...

journal_title：Physical biology

authors： Börner U,Deutsch A,Bär M

更新日期：2006-06-23 00:00:00

abstract：:Chemotaxis is the process by which cells sense changes in their chemical environment and move towards more favorable conditions. In divergent species of bacteria, the chemotaxis proteins localize to the poles of the cell and information is transferred to the flagellar motors through the phosphorylation of a soluble pr...

journal_title：Physical biology

authors： Rao CV,Kirby JR,Arkin AP

更新日期：2005-07-14 00:00:00

abstract：:Electrostatic interaction is the driving force for the encapsulation by virus coat proteins of nanoparticles such as quantum dots, gold particles and magnetic beads for, e.g., imaging and therapeutic purposes. In recent experimental work, Daniel et al (2010 ACS Nano 4 3853-60) found the encapsulation efficiency to sen...

journal_title：Physical biology

authors： Lin HK,van der Schoot P,Zandi R

更新日期：2012-12-01 00:00:00