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At least 235 records · Page 13Linked to original sources

Distributions of Triplets in Genetic Sequences

Distributions of triplets in some genetic sequences are examined and found to be well described by a 2-parameter Markov process with a sparse transition matrix. The variances of all the relevant parameters are not large, indicating that most sequences gather in a small region in the parameter space. Different sequences have very near values of the entropy calculated directly from the data and the two parameters characterizing the Markov process fitting the sequence. No relevance with taxonomy or coding/noncoding is clearly observed.

physics.bio-ph↗

Collective motion of organisms in three dimensions

We study a model of flocking in order to describe the transitions during the collective motion of organisms in three dimensions (e.g., birds). In this model the particles representing the organisms are self-propelled, i.e., they move with the same absolute velocity. In addition, the particles locally interact by choosing at each time step the average direction of motion of their neighbors and the effects of fluctuations are taken into account as well. We present the first results for large scale flocking in the presence of noise in three dimensions. We show that depending on the control parameters both disordered and long-range ordered phases can be observed. The corresponding phase diagram has a number of features which are qualitatively different from those typical for the analogous equilibrium models.

physics.bio-ph↗

SOC in a population model with global control

We study a plant population model introduced recently by J. Wallinga [OIKOS {\bf 74}, 377 (1995)]. It is similar to the contact process (`simple epidemic', `directed percolation'), but instead of using an infection or recovery rate as control parameter, the population size is controlled directly and globally by removing excess plants. We show that the model is very closely related to directed percolation (DP). Anomalous scaling laws appear in the limit of large populations, small densities, and long times. These laws, associated critical exponents, and even some non-universal parameters, can be related to those of DP. As in invasion percolation and in other models where the rôles of control and order parameters are interchanged, the critical value $p_c$ of the wetting probability $p$ is obtained in the scaling limit as singular point in the distribution of infection rates. We show that a mean field type approximation leads to a model studied by Y.C. Zhang et al. [J. Stat. Phys. {\bf 58}, 849 (1990)]. Finally, we verify the claim of Wallinga that family extinction in a marginally surviving population is governed by DP scaling laws, and speculate on applications to human mitochondrial DNA.

cond-mat.stat-mech↗

Punctuated equilibrium in an evolving bacterial population

Recently, Lenski et al have carried out an experiment on bacterial evolution. Their findings support the theory of punctuated equilibrium in biological evolution. We show that the M=2 Bak-Sneppen model can explain some of the experimental results in a qualitative manner.

cond-mat.stat-mech↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗