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At least 703 records · Page 39Linked to original sources

arXiv1999

Effect of shape anisotropy on transport in a 2-dimensional computational model: Numerical simulations showing experimental features observed in biomembranes

We propose a 2-d computational model-system comprising a mixture of spheres and the objects of some other shapes, interacting via the Lennard-Jones potential. We propose a reliable and efficient numerical algorithm to obtain void statistics. The void distribution, in turn, determines the selective permeability across the system and bears a remarkable similarity with features reported in certain biological experiments.

physics.comp-ph↗

arXiv1999

A Model for the Thermodynamics of Globular Proteins

Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water interactions. The model contains both hot and cold folding transitions. In addition it predicts a critical point at a given temperature and chemical potential of the surrounding water. The universality class of this critical point is new.

cond-mat↗

arXiv1999

Complexation of DNA with Cationic Surfactant

Transfection of an anionic polynucleotide through a negatively charged membrane is an important problem in genetic engineering. The direct association of cationic surfactant to DNA decreases the effective negative charge of the nucleic acid, allowing the DNA-surfactant complex to approach a negatively charged membrane. The paper develops a theory for solutions composed of polyelectrolyte, salt, and ionic surfactant. The theoretical predictions are compared with the experimental measurements.

cond-mat↗

arXiv1999

Charge inversion in DNA-amphiphile complexes: Possible application to gene therapy

We study a complex formation between the DNA and cationic amphiphilic molecules. As the amphiphile is added to the solution containing DNA, a cooperative binding of surfactants to the DNA molecules is found. This binding transition occurs at specific density of amphiphile, which is strongly dependent on the concentration of the salt and on the hydrophobicity of the surfactant molecules. We find that for amphiphiles which are sufficiently hydrophobic, a charge neutralization, or even charge inversion of the complex is possible. This is of particular importance in applications to gene therapy, for which the functional delivery of specific base sequence into living cells remains an outstanding problem. The charge inversion could, in principle, allow the DNA-surfactant complexes to approach negatively charged cell membranes permitting the transfection to take place.

cond-mat↗

arXiv2001

RNA Folding and Large N Matrix Theory

We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is set up in such a way that the limit $N\to \infty$ yields the so-called secondary structure (Hartree theory). Tertiary structure and pseudo-knots are obtained by calculating the $1/N^2$ corrections to the partition function. We propose a generalization of the Hartree recursion relation to generate the tertiary structure.

cond-mat.stat-mech↗

arXiv1997

Parallel computing and molecular dynamics of biological membranes

In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on the possible programming strategies. Liquids can be very satisfactorily simulated using the "systolic" method. For more complex systems, like the biological ones at which we are ultimately interested in, the "domain decomposition" approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of elementary components of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed.

physics.bio-ph↗

arXiv2000

Time series model based on global structure of complete genome

A time series model based on the global structure of the complete genome is proposed. Three kinds of length sequences of the complete genome are considered. The correlation dimensions and Hurst exponents of the length sequences are calculated. Using these two exponents, some interesting results related to the problem of classification and evolution relationship of bacteria are obtained.

physics.bio-ph↗

arXiv2003

Fractal Rigidity in Migraine

We study the middle cerebral artery blood flow velocity (MCAfv) in humans using transcranial Doppler ultrasonography (TCD). Scaling properties of time series of the axial flow velocity averaged over a cardiac beat interval may be characterized by two exponents. The short time scaling exponent (STSE) determines the statistical properties of fluctuations of blood flow velocities in short-time intervals while the Hurst exponent describes the long-term fractal properties. In many migraineurs the value of the STSE is significantly reduced and may approach that of the Hurst exponent. This change in dynamical properties reflects the significant loss of short-term adaptability and the overall hyperexcitability of the underlying cerebral blood flow control system. We call this effect fractal rigidity.

physics.bio-ph↗

arXiv1997

Neuro-flow Dynamics and the Learning Processes

A new description of the neural activity is introduced by the neuro-flow dynamics and the extended Hebb rule. The remarkable characteristics of the neuro-flow dynamics, such as the primacy and the recency effect during awakeness or sleep, are pointed out.

cond-mat.dis-nn↗

arXiv1999

Dimensions of fractals related to languages defined by tagged strings in complete genomes

A representation of frequency of strings of length K in complete genomes of many organisms in a square has led to seemingly self-similar patterns when K increases. These patterns are caused by under-represented strings with a certain "tag"-string and they define some fractals when K tends to infinite. The Box and Hausdorff dimensions of the limit set are discussed. Although the method proposed by Mauldin and Williams to calculate Box and Hausdorff dimension is valid in our case, a different and simpler method is proposed in this paper.

physics.bio-ph↗

arXiv2000

A time series model of CDS sequences in complete genome

A time series model of CDS sequences in complete genome is proposed. A map of DNA sequence to integer sequence is given. The correlation dimensions and Hurst exponents of CDS sequences in complete genome of bacteria are calculated. Using the average of correlation dimensions, some interesting results are obtained.

physics.bio-ph↗

arXiv2001

Maximum pull out force on DNA hybrids

We discuss theoretically the force F between two colloidal particles, each of them carrying one single strand DNA. The two strands are complementary only on a finite sequence of consecutive base pairs. We define an adjustment length (a few base pairs): in the adjustment regions near both ends of the paired region, the tension is still mainly on one single strand. But in the central part, the two backbones are equally loaded. This leads to a rupture force, increasing linearly with length, and saturating for large lengths.

physics.bio-ph↗

arXiv2000

Nonlinear denoising of transient signals with application to event related potentials

We present a new wavelet based method for the denoising of {\it event related potentials} ERPs), employing techniques recently developed for the paradigm of deterministic chaotic systems. The denoising scheme has been constructed to be appropriate for short and transient time sequences using circular state space embedding. Its effectiveness was successfully tested on simulated signals as well as on ERPs recorded from within a human brain. The method enables the study of individual ERPs against strong ongoing brain electrical activity.

physics.data-an↗

arXiv2001

Equations for Stochastic Macromolecular Mechanics of Single Proteins: Equilibrium Fluctuations, Transient Kinetics and Nonequilibrium Steady-State

A modeling framework for the internal conformational dynamics and external mechanical movement of single biological macromolecules in aqueous solution at constant temperature is developed. Both the internal dynamics and external movement are stochastic; the former is represented by a master equation for a set of discrete states, and the latter is described by a continuous Smoluchowski equation. Combining these two equations into one, a comprehensive theory for the Brownian dynamics and statistical thermodynamics of single macromolecules arises. This approach is shown to have wide applications. It is applied to protein-ligand dissociation under external force, unfolding of polyglobular proteins under extension, movement along linear tracks of motor proteins against load, and enzyme catalysis by single fluctuating proteins. As a generalization of the classic polymer theory, the dynamic equation is capable of characterizing a single macromolecule in aqueous solution, in probabilistic terms, (1) its thermodynamic equilibrium with fluctuations, (2) transient relaxation kinetics, and most importantly and novel (3) nonequilibrium steady-state with heat dissipation. A reversibility condition which guarantees an equilibrium solution and its thermodynamic stability is established, an H-theorem like inequality for irreversibility is obtained, and a rule for thermodynamic consistency in chemically pumped nonequilibrium steady-state is given.

physics.bio-ph↗

arXiv1998

Entropic Elasticity of Twist-Storing Polymers

We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to an applied torque through the relation Lk = Tw + Wr. We explore this coupling and find agreement between the predictions of our model and recent experimental results on single lambda-DNA molecules. This analysis affords an experimental determination of the microscopic twist stiffness (averaged over a helix repeat). Quantitative agreement between theory and experiment is obtained using C=109 nm. The theory further predicts a thermal reduction of the effective twist rigidity induced by bend fluctuations. Finally, we find a small reflection of molecular chirality in the experimental data and interpret it in terms of a twist-stretch coupling of the DNA duplex.

cond-mat.soft↗

arXiv2000

Self-Assembly in Mixtures of Polymers and Small Associating Molecules

The interaction between a flexible polymer in good solvent and smaller associating solute molecules such as amphiphiles (surfactants) is considered theoretically. Attractive correlations, induced in the polymer because of the interaction, compete with intra-chain repulsion and eventually drive a joint self-assembly of the two species, accompanied by partial collapse of the chain. Results of the analysis are found to be in good agreement with experiments on the onset of self-assembly in diverse polymer-surfactant systems. The threshold concentration for self-assembly in the mixed system (critical aggregation concentration, cac) is always lower than the one in the polymer-free solution (critical micelle concentration, cmc). Several self-assembly regimes are distinguished, depending on the effective interaction between the two species. For strong interaction, corresponding experimentally to oppositely charged species, the cac is much lower than the cmc. It increases with ionic strength and depends only weakly on polymer charge. For weak interaction, the cac is lower but comparable to the cmc, and the two are roughly proportional over a wide range of cmc values. Association of small molecules with amphiphilic polymers exhibiting intra-chain aggregation (polysoaps) is gradual, having no sharp onset.

cond-mat.soft↗

arXiv2003

Dipole relaxation losses in DNA

The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the appreciable AC conductivity of DNA is not due to photon activated hopping between localized states, but instead due to dissipation from dipole motion in the surrounding water helix. Such a result, where the conductivity is due to the constrained motion of overdamped dipoles, reconciles the vanishing DC conductivity of DNA with the considerable AC response.

cond-mat.dis-nn↗

arXiv1998

Analysis of a Population Genetics Model with Mutation, Selection, and Pleiotropy

We investigate the behavior of a population genetics model introduced by Waxman and Peck incorporating mutation, selection, and pleiotropy. The population is infinite and continuous variation of genotype is allowed. Nonetheless, Waxman and Peck showed that if the degree of pleiotropy is large enough,in this model a nonzero fraction of the population can have identical alleles. This `condensed mode' behavior appears in the limit of infinite times. This paper explores the time-dependence of the distribution of alleles in this model. First, the model is analyzed using a recursion technique which enables the distribution of alleles to be calculated at finite times as well as in Waxman and Peck's infinite-time limit. Second, both Waxman and Peck's original model and a related model in which mutations occur continuously are mapped onto problems in quantum mechanics. In both cases, the long-time analysis for the biological model is equivalent to finding the nature of the eigenstates of the quantum problem. The condensed mode appears if and only if there is no bound state in the quantum problem. We compare the behavior of the discrete- and continuous-time versions of the model. The results for the two cases are qualitatively similar, though there are some quantitative differences. We also discuss our attempts to correlate the statistics of DNA sequence variations with the degree of pleiotropy of various genes.

cond-mat↗