Manipulation of in vitro collagen matrix architecture for scaffolds of improved physiological relevance.

abstract：:Circular DNA in viruses and bacteria is often knotted. While mathematically problematic, the determination of the knot size is crucial for the study of the physical and biological behaviour of long macromolecules. Here, we review work on the size distribution of these knots under equilibrium conditions. We discuss kno...

journal_title：Physical biology

authors： Orlandini E,Stella AL,Vanderzande C

更新日期：2009-07-01 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：:Traditional experimental biology has provided a mechanistic understanding of cancer in which the malignancy develops through the acquisition of mutations that disrupt cellular processes. Several drugs developed to target such mutations have now demonstrated clinical value. These advances are unequivocal testaments to ...

journal_title：Physical biology

authors： Stites EC

更新日期：2013-04-01 00:00:00

abstract：:This special issue consists of 11 original papers that elaborate on work presented at the Fourth Annual q-bio Conference on Cellular Information Processing, which was held on the campus of St John's College in Santa Fe, New Mexico, USA, 11-14 August 2010. Now in its fourth year, the q-bio conference has changed consid...

journal_title：Physical biology

authors： Nemenman I,Faeder JR,Hlavacek WS,Jiang Y,Wall ME,Zilman A

更新日期：2011-10-01 00:00:00

abstract：:Peptoids of alpha- and beta-peptides (alpha- and beta-peptoids) can be obtained by shifting the amino acid side chains from the backbone carbon atoms of the monomer constituents to the peptide nitrogen atoms. They are, therefore, N-substituted poly-glycines and poly-beta-alanines, respectively. Due to the substituted ...

journal_title：Physical biology

authors： Baldauf C,Günther R,Hofmann HJ

更新日期：2006-02-02 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：:Neurofilaments are transported along axons stochastically in a stop-and-go manner, cycling between brief bouts of rapid movement and pauses that can vary from seconds to hours in length. Presently the only way to analyze neurofilament pausing experimentally on both long and short time scales is the pulse-escape method...

journal_title：Physical biology

authors： Li Y,Brown A,Jung P

更新日期：2014-04-01 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：: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：: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：:Lipid molecules, structural components of biomembranes, have been proposed for an important role in membrane fusion. Through various techniques based on a protein-reconstituted vesicle-vesicle fusion system, we investigated the influence of several lipid molecules on different stages of a yeast soluble N-ethylmaleimid...

journal_title：Physical biology

authors： Lai Y,Zhao L,Bu B,Lou X,Li D,Ji B,Liu J,Diao J,Shin YK

更新日期：2015-04-21 00:00:00

abstract：:Particle tracking offers significant insight into the molecular mechanics that govern the behavior of living cells. The analysis of molecular trajectories that transition between different motive states, such as diffusive, driven and tethered modes, is of considerable importance, with even single trajectories containi...

journal_title：Physical biology

authors： Young DC,Scrimgeour J

更新日期：2018-07-06 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：:In Parkinson's disease (PD), there is evidence that alpha-synuclein (alphaSN) aggregation is coupled to dysfunctional or overburdened protein quality control systems, in particular the ubiquitin-proteasome system. Here, we develop a simple dynamical model for the on-going conflict between alphaSN aggregation and the m...

journal_title：Physical biology

authors： Sneppen K,Lizana L,Jensen MH,Pigolotti S,Otzen D

更新日期：2009-05-01 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：: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：: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：: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：: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：:The importance of the tumor microenvironment in cancer progression is undisputed, yet the significance of biophysical forces in the microenvironment remains poorly understood. Interstitial fluid flow is a nearly ubiquitous and physiologically relevant biophysical force that is elevated in tumors because of tumor-assoc...

journal_title：Physical biology

authors： Shieh AC,Swartz MA

更新日期：2011-02-01 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：:We study the applicability of Van Kampen's linear noise approximation to the calculation of fluctuations in cells due to small number of molecules for simple genetic systems not previously considered. These systems include dimer formation and feedback. We explain why the linear noise approximation can be surprisingly ...

journal_title：Physical biology

authors： Hayot F,Jayaprakash C

更新日期：2004-12-01 00:00:00

abstract：:In addition to serving as structural elements and as tracks for motor proteins, microtubules use chemical energy derived from the hydrolysis of GTP to generate forces when growing and shrinking. These forces are used to push or pull on organelles such as chromosomes and the mitotic spindle. If an array of microtubules...

journal_title：Physical biology

authors： Howard J

更新日期：2006-02-28 00:00:00

abstract：:Cancer cells are known to modify their micro-environment such that it can sustain a larger population, or, in ecological terms, they construct a niche which increases the carrying capacity of the population. It has however been argued that niche construction, which benefits all cells in the tumour, would be selected a...

journal_title：Physical biology

authors： Gerlee P,Anderson AR

更新日期：2015-08-12 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：:The study on aerial plant organs (leaves and stems) motions is reviewed. The history of observations and studies is put in the perspective of the ideas surrounding them, leading to a presentation of the current classification of these motions. After showing the shortcomings of such a classification, we present, follow...

journal_title：Physical biology

authors： Rivière M,Derr J,Douady S

更新日期：2017-08-21 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：: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：: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：:How cell collectives move and deposit subunits within a developing embryo is a question of outstanding interest. In many cases, a chemotactic mechanism is employed, where cells move up or down a previously generated attractive or repulsive gradient of signalling molecules. Recent studies revealed the existence of syst...

journal_title：Physical biology

authors： Streichan SJ,Valentin G,Gilmour D,Hufnagel L

更新日期：2011-08-01 00:00:00