Chemical kinetic mechanistic models to investigate cancer biology and impact cancer medicine.

abstract：:Bidirectional cargo transport by molecular motors in cells is a complex phenomenon in which the cargo (usually a vesicle) alternately moves in retrograde and anterograde directions. In this case, teams of oppositely pulling motors (e.g., kinesin and dynein) bind to the cargo, simultaneously, and 'coordinate' their act...

journal_title：Physical biology

authors： Bhat D,Gopalakrishnan M

更新日期：2012-08-01 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：:Voltage-dependent ion channels determine the electric properties of axonal cell membranes. They not only allow the passage of ions through the cell membrane, but also contribute to an additional charging of the cell membrane resulting in the so-called capacitance loading. The switching of the channel gates between an ...

journal_title：Physical biology

authors： Schmid G,Goychuk I,Hänggi P

更新日期：2006-11-22 00:00:00

abstract：:A model of ligand-induced intracellular calcium (Ca2+) responses incorporating phospholipase C (PLC) and protein kinase C (PKC) is developed for the purpose of understanding the mechanisms underlying the observed temporal patterns of intracellular calcium (Ca(i)2+) under sustained agonist stimulation. Some studies hav...

journal_title：Physical biology

authors： Kang M,Othmer HG

更新日期：2007-12-13 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：: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：: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：:The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounte...

journal_title：Physical biology

authors： Rader AJ

更新日期：2009-12-11 00:00:00

abstract：:We present a new particle tracking software algorithm designed to accurately track the motion of low-contrast particles against a background with large variations in light levels. The method is based on a polynomial fit of the intensity around each feature point, weighted by a Gaussian function of the distance from th...

journal_title：Physical biology

authors： Rogers SS,Waigh TA,Zhao X,Lu JR

更新日期：2007-10-09 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：: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

abstract：:The controlling factors that underlie the growth of tumors have often been hard to identify because of the presence in this system of a large number of intracellular biochemical parameters. Here, we propose a simplifying framework to identify the key physical parameters that govern the early growth of tumors. We model...

journal_title：Physical biology

authors： Remy G,Cluzel P

更新日期：2016-04-04 00:00:00

abstract：:Cells can often choose among several stably heritable phenotypes. Examples are the expressions of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states that may be associated with positive feedback in dynamic modification of nucleosomes. We generalize thi...

journal_title：Physical biology

authors： Micheelsen MA,Mitarai N,Sneppen K,Dodd IB

更新日期：2010-06-04 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：:This paper explores the potential for simplicity to reveal new biological understanding. Borrowing selectively from physics thinking, and contrasting with Crick's reductionist philosophy, the author argues that greater emphasis on simplicity is necessary to advance biology and its applications. ...

journal_title：Physical biology

authors： Newman T

更新日期：2015-12-30 00:00:00

abstract：:The translocation of molecules across cellular membranes or through synthetic nanopores is strongly affected by thermal fluctuations. In this work we study how the dynamics of a polymer in a noisy environment changes when the translocation process is driven by an oscillating electric field. An improved version of the ...

journal_title：Physical biology

authors： Pizzolato N,Fiasconaro A,Adorno DP,Spagnolo B

更新日期：2010-08-04 00:00:00

abstract：:Branching morphogenesis is a widely spread phenomenon in nature. In organogenesis, it results from the inhomogeneous growth of the epithelial sheet, leading to its repeated branching into surrounding mesoderm. Lung morphogenesis is an emblematic example of tree-like organogenesis common to most mammals. The core signa...

journal_title：Physical biology

authors： Clément R,Douady S,Mauroy B

更新日期：2012-12-01 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：: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：:Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence...

journal_title：Physical biology

authors： Mitarai N,Pedersen S

更新日期：2013-10-01 00:00:00

abstract：:In many bacterial species, the protein FtsZ forms a cytoskeletal ring that marks the future division site and scaffolds the division machinery. In rod-shaped bacteria, most frequently membrane-attached FtsZ rings or ring fragments are reported and occasionally helices. By contrast, axial FtsZ clusters have never been ...

journal_title：Physical biology

authors： Fischer-Friedrich E,Friedrich BM,Gov NS

更新日期：2012-02-01 00:00:00

abstract：:This report presents a simple model that describes the motion of a single Dictyostelium discoideum cell exposed to a traveling wave of cyclic adenosine monophosphate (cAMP). The model incorporates two types of responses to stimulation by cAMP: the changes in the polarity and motility of the cell. The periodic change i...

journal_title：Physical biology

authors： Ishiwata R,Iwasa M

更新日期：2015-03-19 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：: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：:The field of tissue engineering aims to produce living, biological constructs which possess the appropriate spatial ordering of cells and their extra cellular matrix products. The complexity of a single cell and its interactions in a large collective have made development of useful models to assist in tissue culture d...

journal_title：Physical biology

authors： Pietak A,Waldman SD

更新日期：2008-04-01 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：:The majority of chronic infections are caused by biofilms, which have higher levels of antibiotic resistance than planktonic growth. Violet-blue 405 nm light has recently emerged as a novel bactericide, but limited studies have been conducted on its effectiveness against biofilms. We found that in response to 405 nm l...

journal_title：Physical biology

authors： Blee JA,Roberts IS,Waigh TA

更新日期：2020-03-04 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：: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 glycolytic enzyme pyruvate kinase M2 (PKM2) exists in both catalytically inactive dimeric and active tetrameric forms. In cancer cells, PKM2 dimer predominance contributes to tumor growth by triggering glycolytic reprogramming. However, the mechanism that promotes PKM2 dimer predominance over tetramer in cancer ce...

journal_title：Physical biology

authors： Shi X,You L,Luo RY

更新日期：2019-09-18 00:00:00