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At least 559 records · Page 31Linked to original sources
arXiv1997

Do Topological Charge Solitons Participate in DNA Activity?

We present a novel electromagnetic model of DNA molecules, in which the P-bonds act as tunnel junctions and the H-bonds as capacitors. Excess charge in the model gives rise to two coupled modified sine-Gordon equations, which admit topological solitonic excitations. We study the dynamics of the solitons, their effect on the DNA transport properties, and comment about their role in the DNA functioning. We propose specific experiments in order to test our predictions.

physics.bio-ph↗
arXiv1998

The Hierarchy of Fast Motions in Protein Dynamics

For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the system in order to increase the time step. An accurate knowledge of these motions is a necessary prerequisite for such efforts. It is known that harmonic vibrations of bond lengths and bond angles produce the highest frequencies in proteins. There are also fast anharmonic motions, such as inter-atomic collisions, which are probably most important when bond lengths and bond angles are fixed. However, the specific time scales corresponding to all these limitations are not known precisely. In order to clarify the above issue this paper analyses time step limiting factors in a series of numerical tests by using an internal coordinate molecular dynamics approach, which allows chosen internal coordinates to be frozen. It is found that, in proteins, there is a rather complicated hierarchy of fast motions, with both harmonic and anharmonic effects mixed together at several close time scales. Non-bonded interactions, notably strong hydrogen bonding, create locally distributed normal modes with frequencies similar to those of bond stretching between non-hydrogen atoms. They also impose ubiquitous anharmonic limitations starting from rather small step sizes. With fixed standard amino acid geometry, rotations of hydrogen bonded hydroxyl groups limit time steps at the 5 fsec level. The next important limitation occurs around 10 fsec and is created by collisions between non-hydrogen atoms.

physics.comp-ph↗
arXiv1998

Scaling Laws and Similarity Detection in Sequence Alignment with Gaps

We study the problem of similarity detection by sequence alignment with gaps, using a recently established theoretical framework based on the morphology of alignment paths. Alignments of sequences without mutual correlations are found to have scale-invariant statistics. This is the basis for a scaling theory of alignments of correlated sequences. Using a simple Markov model of evolution, we generate sequences with well-defined mutual correlations and quantify the fidelity of an alignment in an unambiguous way. The scaling theory predicts the dependence of the fidelity on the alignment parameters and on the statistical evolution parameters characterizing the sequence correlations. Specific criteria for the optimal choice of alignment parameters emerge from this theory. The results are verified by extensive numerical simulations.

physics.bio-ph↗
arXiv1998

First experimental tests of the Peyrard-Bishop model applied to the melting of very short DNAs

The melting curves of short heterogeneous DNA chains in solution are calculated on the basis of statistical thermodynamics and compared to experiments. The computation of the partition function is based on the Peyrard-Bishop hamiltonian, which has already been adopted in the theoretical description of the melting of long DNA chains. In the case of short chains it is necessary to consider not only the breaking of the hydrogen bonds between single base pairs, but also the complete dissociation of the two strands forming the double helix.

physics.bio-ph↗
arXiv1998

Discrimination of the Healthy and Sick Cardiac Autonomic Nervous System by a New Wavelet Analysis of Heartbeat Intervals

We demonstrate that it is possible to distinguish with a complete certainty between healthy subjects and patients with various dysfunctions of the cardiac nervous system by way of multiresolutional wavelet transform of RR intervals. We repeated the study of Thurner et al on different ensemble of subjects. We show that reconstructed series using a filter which discards wavelet coefficients related with higher scales enables one to classify individuals for which the method otherwise is inconclusive. We suggest a delimiting diagnostic value of the standard deviation of the filtered, reconstructed RR interval time series in the range of $\sim 0.035$ (for the above mentioned filter), below which individuals are at risk.

physics.med-ph↗
arXiv1998

The geometry of the Fisher selection dynamics

We study the Fisher model describing natural selection in a population with a diploid structure of a genome by differential- geometric methods. For the selection dynamics we introduce an affine connection which is shown to be the projectively Euclidean and the equiaffine one. The selection dynamics is reformulated similar to the motion of an effective particle moving along the geodesic lines in an 'effective external field' of a tensor type. An exact solution is found to the Fisher equations for the special case of fitness matrix associated to the effect of chromosomal imprinting of mammals. Biological sense of the differential- geometric constructions is discussed. The affine curvature is considered as a direct consequence of an allele coupling in the system. This curving of the selection dynamics geometry is related to an inhomogenity of the time flow in the course of the selection.

physics.bio-ph↗
arXiv1998

Nearly Closed Loops in Biological Systems as Electromagnetic Receptors

It is noted here that when a nearly closed loop in a biological system, such as a self-synapsing (autapsing) neuron or mutually synapsing pair, is exposed to an AC magnetic field, the induced electric fields in the insulating gaps can be many orders of magnitude larger than the average values typically discussed in the literature.$^{1,2}$ It is suggested that animal nervous systems might possibly be affected in selected spots by man-made alternating magnetic fields at weaker levels than previously supposed. Radio and microwave radiation should be considered particularly suspect.

physics.bio-ph↗
arXiv1998

Tertiary structure prediction of C-peptide of ribonuclease A by multicanonical algorithm

We have performed multicanonical Monte Carlo simulations of C-peptide of ribonuclease A. It is known by CD and NMR experiments that this peptide has high alpha-helix content in aqueous solution and that the side-chain charges of residues Glu-2$^-$ and His-12$^+$ play an important role in the stability of the alpha-helix. In order to confirm these experimental implications, we have used two analogues of the peptide with charged and neutral side chains of Glu-2 and His-12. Two dielectric functions, distance-dependent and constant, are considered to study the effects of solvent contributions. All the simulations were started from random initial conformations. Various thermodynamic quantities such as average helicity as a function of residue number and average distance between two side chains as a function of temperature are calculated. The results are found to be in accord with the implications of CD and NMR experiments. The lowest-energy conformation obtained has an alpha-helix from Ala-4 to Gln-11 in complete agreement with the corresponding structure deduced from an X-ray crystallography experiment of ribonuclease A. It is shown that the salt bridge between the side chains of Glu-2$^-$ and Arg-10$^+$, which is known to exist from both NMR and X-ray experiments, is formed only when the side chains are properly charged. Its formation is greatly enhanced when the distance-dependent dielectric function is used.

physics.chem-ph↗
arXiv1998

Kinetics properties of voltage induced colicin Ia channels into a lipid bilayer

The activation kinetics of the ion channels formed by colicin Ia incorporated into a planar bilayer lipid membrane (BLM) was investigated by the voltage clamp technique using different step voltage stimuli. The temporal behaviour of ion channels put in evidence a gain or a loss of memory, revealed by a specific sequence of electrical pulses used for stimulation.

physics.bio-ph↗
arXiv1998

Hydrophobic Effects on a Molecular Scale

A theoretical approach is developed to quantify hydrophobic hydration and interactions on a molecular scale, with the goal of gaining insight into the molecular origins of hydrophobic effects. The model is based on the fundamental relation between the probability for cavity formation in bulk water resulting from molecular-scale density fluctuations, and the hydration free energy of the simplest hydrophobic solute, a hard particle. This probability is estimated using an information theory (IT) approach, incorporating experimentally available properties of bulk water -- the density and radial distribution function. The IT approach reproduces the simplest hydrophobic effects: hydration of spherical nonpolar solutes, the potential of mean force between methane molecules, and solvent contributions to the torsional equilibrium of butane. Applications of this approach to study temperature and pressure effects provide new insights into the thermodynamics and kinetics of protein folding. The IT model relates the hydrophobic-entropy convergence observed in protein unfolding experiments to the macroscopic isothermal compressibility of water. A novel explanation for pressure denaturation of proteins follows from an analysis of the pressure stability of hydrophobic aggregates, suggesting that water penetrates the hydrophobic core of proteins at high pressures. This resolves a long-standing puzzle, whether pressure denaturation contradicts the hydrophobic-core model of protein stability. Finally, issues of ``dewetting'' of molecularly large nonpolar solutes are discussed in the context of a recently developed perturbation theory approach.

physics.chem-ph↗
arXiv1998

A dynamic programming algorithm for RNA structure prediction including pseudoknots

We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the algorithm is complex, which led us to adopt a useful graphical representation (Feynman diagrams) borrowed from quantum field theory. We present an implementation of the algorithm that generates the optimal minimum energy structure for a single RNA sequence, using standard RNA folding thermodynamic parameters augmented by a few parameters describing the thermodynamic stability of pseudoknots. We demonstrate the properties of the algorithm by using it to predict structures for several small pseudoknotted and non-pseudoknotted RNAs. Although the time and memory demands of the algorithm are steep, we believe this is the first algorithm to be able to fold optimal (minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model.

physics.bio-ph↗
arXiv1998

Systematics of the Genetic Code and Anticode: History, Supersymmetry, Degeneracy and Periodicity

Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the genetic code, and the periodicity of many amino acid physico-chemical properties. Such factors are analysed in the context of a $sl(6/1)$ supersymmetric model of the genetic code.

physics.bio-ph↗
arXiv1998

A Theory for the Membrane Potential of Living Cells

We give an explicit formula for the membrane potential of cells in terms of the intracellular and extracellular ionic concentrations, and derive equations for the ionic currents that flow through channels, exchangers and electrogenic pumps. We demonstrate that the work done by the pumps equals the change in potential energy of the cell, plus the energy lost in downhill ionic fluxes through the channels and exchangers. The theory is illustrated in a simple model of spontaneously active cells in the cardiac pacemaker. The model predicts the experimentally observed intracellular ionic concentration of potassium, calcium, and sodium. Likewise the shapes of the simulated action potential and five membrane currents are in good agreement with experiments. We do not see any drift in the values of the concentrations in a long time simulation, and we obtain the same asymptotic values when starting from the full equilibrium situation with equal intracellular and extracellular ionic concentrations.

physics.bio-ph↗
arXiv1998

Evolution in time-dependent fitness landscapes

Evolution in changing environments is an important, but little studied aspect of the theory of evolution. The idea of adaptive walks in fitness landscapes has triggered a vast amount of research and has led to many important insights about the progress of evolution. Nevertheless, the small step to time-dependent fitness landscapes has most of the time not been taken. In this work, some elements of a theory of adaptive walks on changing fitness landscapes are proposed, and are subsequently applied to and tested on a simple family of time-dependent fitness landscapes, the oscillating NK landscapes, also introduced here. For these landscapes, the parameter governing the evolutionary dynamics is the fraction of static fitness contributions f_S. For small f_S, local optima are virtually non-existent, and the adaptive walk constantly encounters new genotypes, whereas for large f_S, the evolutionary dynamics reduces to the one on static fitness landscapes. Evidence is presented that the transition between the two regimes is a 2nd order phase transition akin a percolation transition. For f_S close to the critical point, a rich dynamics can be observed. The adaptive walk gets trapped in noisy limit cycles, and transitions from one noisy limit cycle to another occur sporadically.

physics.bio-ph↗
arXiv1998

Elastic Properties of Nematic Liquid Crystals Formed by Living and Migrating Cells

In culture migrating and interacting amoeboid cells can form nematic liquid crystal phases. A polar nematic liquid crystal is formed if the interaction has a polar symmetry. One type of white blood cells (granulocytes) form clusters where the cells are oriented towards the center. The core of such an orientational defect (disclination) is either a granulocyte forced to be in an isotropic state or another cell type like a monocyte. An apolar nematic liquid crystal is formed if the interaction has an apolar symmetry. Different cell types like human melanocytes (=pigment cells of the skin), human fibroblasts (=connective tissue cells), human osteoblasts (=bone cells), human adipocytes (= fat cells) etc., form an apolar nematic liquid crystal. The orientational elastic energy is derived and the orientational defects (disclination) of nematic liquid crystals are investigated. The existence of half-numbered disclinations show that the nematic phase has an apolar symmetry. The density- and order parameter dependence of the orientational elastic constants and their absolute values are estimated. From the defect structure, one finds that the splay elastic constant is smaller than the bend elastic constant (melanocytes). The core of a disclination is either a cell free space or occupied by non oriented cells (isotropic phase) or occupied by a cell with a different symmetry or occupied by another cell type.

physics.bio-ph↗