Download Statistical mechanical theory of DNA denaturation. - S Homma Affiliation: School of Engineering, Gunma University, Kiryu, 376-8515 Japan. | ePub
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The melting curve for a covalently closed circular dna has been analyzed on the hasis of an statistical mechanics indicate close agreement with the available.
3 d1 о d3 specified by a constitutive relation, which generalizes euler-bernouilli beam theory.
For instance, the transport of rna across the nuclear pore or the injection of viral dna plasmid by bacteriophages into a bacteria.
We present evidence supporting the idea that the dna sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range-indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene; we utilize this fact to build a coding sequence finder algorithm, which uses.
The eigenfunctions for circular boundary conditions of the differential equation first used by harris and hearst in 1966 to represent the dynamic properties of the wormlike coil have now been applied to the closed circular coils of high writhe. In order to avoid problems of knotting and excluded volume, the discussion here has been restricted to three‐dimensional eigenfunctions with near.
Jan 14, 2013 a theoretical study of the role of bulk crowders on target search dynamics of dna binding proteins.
However, distinctions in the mechanics of dna looping versus cyclization can have profound quantitative effects on the thermodynamics of loop closure. We have extended a statistical mechanical theory recently developed for dna cyclization to model dna looping, taking into account protein flexibility.
The double-helical topology of dna molecules observed at room temperature in the absence of any external loads can be disrupted by increasing the bath.
The book contains a detailed review of classical and quantum mechanics, in-depth discussions of the most commonly used simultaneously with modern computational techniques such as molecular dynamics and monte carlo, and important topics including free-energy calculations, linear-response theory, harmonic baths and the generalized langevin.
The term “thermodynamics” comes from the greek words ‘therme’ and ‘dynamic which means _______.
In this book, a statistical mechanical interpretation of ait is introduced while explaining the basic notions and results of ait to the reader who has an acquaintance with an elementary theory of computation. A simplification of the setting of ait is the noiseless source coding in information theory.
Edu the ads is operated by the smithsonian astrophysical observatory under nasa cooperative agreement nnx16ac86a.
We present a statistical-mechanical selection theory for the sequence analysis of a set of specific dna regulatory sites that makes it possible to predict the relationship between individual base-pair choices in the site and specific activity (affinity).
Motivation: meltsim is a windows-based statistical mechanical program for simulating melting curves of dnas of known sequence and genomic dimensions under different conditions of ionic strength with great accuracy.
02, plectonemic supercoils are stable, but thermal fluctuations continue to play an important role, competing with bending and twisting elastic energy to set the superhelical radius. We have constructed an analytic theory for this effect that agrees well with experiment [3], using methods from polymer statistical mechanics.
Dna topology, elasticity, mechanics, statistical mechanics, stretching. The discovery of dna structure 55 years ago marked the beginning of a process that has transformed the foundations of biology and medicine, and accelerated the development of new fields, such as molecular biology or genetic engineering.
The concept of local composition has received much attention during the past few years, much of which has been devoted to justifying the empirical model proposed by wilson in 1964.
Let us now calculate the binding probability of a tf to a binding site on the dna as a function of the tf concentrations. We assume that the system is in thermodynamic equilibrium and use the framework of statistical mechanics. To this end, consider the more detailed view on the events that determine the kinetics we discussed above.
Nov 30, 2020 this paper discuss its nonlinear dynamics, its statistical mechanics, and one theory combined with the knowledge of the equilibrium statistical.
Classical mechanics covers a set of problems which are a subset of the ones covered by quantum mechanics. Even more clearly is nonrelativistic mechanics a part of relativistic mechanics. Such a statement cannot be made if one tries to relate thermodynamics and statistical mechanics.
Atomic theory was invented by the ancient greek philosophers leucippus and democritus, who speculated that the world essentially consists of myriads of tiny indivisible particles, which theycalled atomsfromthegreek atomonmeaning“uncuttable.
The equations of hydrodynamics—continuity equation, equation of motion, and equation of energy transport—are derived by means of the classical statistical mechanics. Thereby, expressions are obtained for the stress tensor and heat current density in terms of molecular variables.
Electrostatics, statistical mechanics, and dynamics of dna david swigon university of pittsburgh september 2007.
Statistical mechanicswith emphasis on the “statistical,” and least-possible reference to the “mechanics. ” while the mechanical details change from system to system, the statistical digestion of those details is system-independent, and it is that fact that accounts for the compelling universality of thermodynamics.
The theory represents a microscopic-based statistical mechanical approach for penetrant diffusion in polymers and provides a foundation for treating time-dependent penetrant diffusivity in aging polymer glasses, collective effects induced by finite penetrant loading, and diffusion in heterogeneous polymeric materials.
Abstract: a unifying theory of the denaturation transition of dna, driven by temperature t or induced by an external mechanical torque gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular structure.
Dna with high gc-content is more stable than dna with low gc-content. As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of dna in a double helix can thus be pulled apart like a zipper, either by a mechanical force or high temperature.
(pmid:23345673 pmcid:pmc3456599) full text citations bioentities related articles external links j biol.
Statistical mechanical model theory of the stability of o/w and w/o microemulsions.
Dec 27, 2006 applying our recent statistical-mechanical theory for dna looping, we calculated repression as a function of operator spacing (58–156 bp) from.
Ability to map polymerases and nucleosomes on chromatin is important for understanding the impact of chromatin remodeling on key cellular processes. Current methods have produced a wealth of information that demonstrates this importance, but key information is elusive in these methods.
Journal of statistical mechanics: theory and experiment (jstat) is a multi-disciplinary, peer-reviewed international journal created by the international school for advanced studies (sissa) and iop publishing (iop). Jstat covers all aspects of statistical physics, including experimental work that impacts on the subject.
Statistical mechanics of dna-nanotube adsorption shushanik tonoyan, davit khechoyan, yevgeni mamasakhlisov, and artem badasyan phys.
The connection between statistical mechanics on the one side and quantum mechanics and quantum field theory on the other side is based on the analogy between thermal and quantum fluctuations. Formally, the connection is expressed through the mathematical equivalence between the partition function in statistical mechanics and the propagator in quantum field theory.
Mar 18, 2019 twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of dna: perturbation theory and beyond.
Statistical mechanics sets out to explain the behaviour of macroscopic systems by studying the statistical properties of their microscopic constituents.
N2 - the simplest model of dna mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling g between twisting and bending, known to arise from the groove asymmetry of the dna double helix.
Statistical mechanics of coil-hairpin transition in a single stranded dna oligomer arxiv:cond-mat/0701368v1 [cond-mat. Stat-mech] 16 jan 2007 sanjay kumar, debaprasad giri† and yashwant singh department of physics, banaras hindu university, varanasi 221 005, india, † physics section, mmv, banaras hindu university, varanasi 221 005, india.
Attraction between the polycyclic aromatic surface elements of carbon nanotubes (cnt) and the aromatic nucleotides of deoxyribonucleic acid (dna) leads to reversible adsorption (physisorption) between the two, a phenomenon related to hybridization.
Statistical mechanical theory for the plectonemic dna supercoil the dna free of protein must be in a highly reduced configurational entropy state.
A statistical-mechanical model taking account of non-neighboring interactions between base-pairs, sequence-dependent symmetric twisting, tilting, sliding fluctuations and asymmetric rolling fluctuations was proposed to predict dna conformation.
Statistical mechanical theory and molecular simulation provide the link between the properties of molecules and the equilibrium and dynamical properties of bulk matter. These tools are applied both to the pursuit of pure science and to real life, engineering and industrial applications.
Statistical mechanics provides a theoretical bridge that takes you from the micro world1, to the macro world2. The chief architects of the bridge were ludwig eduard boltzmann (1844 - 1906), james clerk maxwell(1831-1879), josiah willard gibbs(1839-1903) and albert einstein(1879-1953).
Final covers parts 1-3 and bcs theory at finite temperature in part 4 course schedule and outline part 1: (ll, pb) foundations: (10 lectures) history, heat, engines, kinetic theory and entropy. Computational methods, molecular dynamics, ensembles, ergodicity.
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