Improvements in continuum modeling for biomolecular systems

Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson–Boltzmann(PB)/Poisson–Nernst–Planck(PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture(or cannot accurately capture)some important physical properties of the biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.     

Formation and interaction of low-energy electrons and biomolecular ions in electrostatic storage ring

The interaction between delta electrons and DNA molecules and other biological structures is one of the important processes taking place in hadron therapy. This paper discusses the formation of low-energy electrons and ions of DNA molecules and other biomolecular ions in an electrostatic storage ring. The results of experimental studies into the interaction between electrons and biomolecular ions for a simulation of the contribution that delta electrons make to the radiation damage of cells in hadron therapy are presented.     

Length measurement in accelerated systems

We investigate the limitations of length measurements by accelerated observers in Minkowski spacetime brought about via the hypothesis of locality, namely, the assumption that an accelerated observer at each instant is equivalent to an otherwise identical momentarily comoving inertial observer. We find that consistency can be achieved only in a rather limited neighborhood around the observer with linear dimensions that are negligibly small compared to the characteristic acceleration length of the observer.     

Summation of electrostatic interactions in quasi-two-dimensional simulations

An error in our previous paper (Clark, A. T., Madden, T. J. and Warren, P. B., 1996 Molec. Phys., 87, 1063) is corrected. This brings the results into agreement with the recent work of Grønbech-Jensen et al. (Grønbech-Jensen, N., Hummer, G. and Beardmore, K. M., Molec. Phys., 1997, 92, 941).     

Screened electrostatic interactions between clay platelets

An effective pair potential for systems of uniformly charged lamellar colloids in the presence of an electrolytic solution of microscopic co- and counterions is derived. The charge distribution on the discs is expressed as a collection of multipole moments, and the tensors which determine the interactions between these multipoles are derived from a screened Coulomb potential. Unlike previous theoretical studies of such systems, the interaction energy may now be expressed for discs at arbitrary mutual orientation. The potential is shown to be exactly equivalent to the use of linearized Poisson–Boltzmann theory.     

Nonlinear oscillations of a charged drop accelerated in an electrostatic field

An analytical asymptotic solution to the problem of nonlinear oscillations of a charged drop moving with acceleration through a vacuum in a uniform electrostatic field is found. The solution is based on a quadratic approximation in two small parameters: the eccentricity of the equilibrium spheroidal shape of the drop and the amplitude of the initial deformation of the equilibrium shape. In the calculations carried out in an inertial frame of reference with the origin at the center of mass of the drop, expansions in fractional powers of the small parameter are used. Corrections to the vibration frequencies are always negative and appear even in the second order of smallness. They depend on the stationary deformation of the drop in the electric field and nonlinearly reduce the surface charge critical for development of the drops’s instability. It is found that the evolutions of the shapes of nonlinearly vibrating unlike-charged drops differ slightly owing to inertial forces.     

Interaction of EHF radiation with biomolecular systems

Data on the absorption of EHF electromagnetic energy by aqueous solutions are summarized. Experimental tests for positive (hydrophilic and hydrophobic) and negative (hydrophilic) hydration are formulated. The applicability of the proposed approach to the study of the hydration of high-molecular-weight systems, including aqueous solutions of proteins, is demonstrated. A model is proposed that explains the interaction of EHF radiation with real biological systems, including under conditions of EHF therapy. The experimental data on the absorption of EHF radiation by aqueous solutions of organic and inorganic electrolytes and nonelectrolytes as well as globular proteins are used to construct a model that explains certain details of EHF therapy. The fraction of mobile water molecules in the skin is considered the primary molecular target for EHF radiation; they are capable of transporting the EHF energy to primary physiological targets of the protein type.Institute of Radio Engineering and Electronics, Russian Academy of Sciences. Institute of Organic Chemistry, Russian Academy of Sciences. Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Radiofizika, Vol. 37, No. 1, pp. 42–55, January, 1994.     

Nonhomogeneous electrostatic oscillations in two-dimensional systems

A new type of excitations — electrostatic oscillations (ESO) — are shown to exist in the finite superlattices (SL). The ESO are the limiting case of the surface magnetoplasmons when the scale length of the spatial variations in the fields and currents is comparable with the sample dimensions. The formal similarity is found between the ESO and the magnetization vibrations in ferromagnetic materials (Walker's modes [1,2]). The main feature of the ESO is the independence of their frequencis on the absolute dimensions of a sample.     

Inductive and electrostatic acceleration in relativistic jet-plasma interactions

We report on the observation of rapid particle acceleration in numerical simulations of relativistic jet-plasma interactions and discuss the underlying mechanisms. The dynamics of a charge-neutral, narrow, electron-positron jet propagating through an unmagnetized electron-ion plasma was investigated using a three-dimensional, electromagnetic, particle-in-cell computer code. The interaction excited magnetic filamentation as well as electrostatic plasma instabilities. In some cases, the longitudinal electric fields generated inductively and electrostatically reached the cold plasma-wave-breaking limit, and the longitudinal momentum of about half the positrons increased by 50% with a maximum gain exceeding a factor of 2 during the simulation period. Particle acceleration via these mechanisms occurred when the criteria for Weibel instability were satisfied.     

Lamellar phase coexistence induced by electrostatic interactions

Membranes containing highly charged biomolecules can have a minimal free-energy state at small separations that originates in the strongly correlated electrostatic interactions mediated by counterions. This phenomenon can lead to a condensed, lamellar phase of charged membranes that coexists in thermodynamic equilibrium with a very dilute membrane phase. Although the dilute phase is mostly water, entropy dictates that this phase must contain some membranes and counterions. Thus, electrostatics alone can give rise to the coexistence of a condensed and an unbound lamellar phase. We use numerical simulations to predict the nature of this coexistence when the charge density of the membrane is large, for the case of multivalent counterions and for a membrane charge that is characteristic of biomolecules. We also investigate the effects of counterion size and salt on the two coexisting phases. With increasing salt concentration, we predict that electrostatic screening by salt can destroy the phase separation.     

Stretching DNA: Role of electrostatic interactions

The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent variational approach. For small values of the external force f, we find the extension scales as where is the Debye screening length. In the limit of large force the electrostatic effects can be accounted for within the semiflexible chain model of DNA by assuming that only small excursions from rod-like conformations are possible. In this regime the extension approaches the contour length as where f is the magnitude of the external force. The theory is used to analyze experiments that have measured the extension of double-stranded DNA subject to tension at various salt concentrations. The theory reproduces nearly quantitatively the elastic response of DNA at small and large values of f and for all concentration of the monovalent counterions. The limitations of the theory are also pointed out. Received 13 October 1998 and Received in final form 9 June 1999     

Magnetic field effects in the presence of electrostatic interactions

Magnetic field effects on ion radical pair (IRP) recombination reactions are considered. In the diffusion approximation simple analytical expressions for the magnitudes of these effects are obtained. They are reduced to those obtained within the simple cage approximation in the case, when the intramolecular spin interactions are strong enough and to those obtained within the free radical approximation in the opposite case. The applicability of both simple approximations are shown to be closely connected with peculiarities of the IRP decay kinetics. Namely, the cage approximation is applicable for the strong spin interactions because the IRP decays exponentially at small times. The free radical approximation is valid in the opposite limit of weak interactions since at large times the IRP decays as a free radical pair.     

Nanowire manipulation on surfaces through electrostatic self‐assembly and magnetic interactions

A method for fabricating aligned nanowire arrays on surfaces is shown. Gold and segmented Au/Ni/Au nanowires of high aspect ratio have been prepared by template electrosynthesis, and functionalized with charged short alkanethiols that can be ionized in aqueous solutions. Different distributions of funtionalized nanowires could be obtained on large surfaces from nanowire aqueous suspensions, avoiding aggregation due to electrical repulsion. Due to the high magnetic anisotropy of segmented Au/Ni/Au nanowires chaining of aligned nanowires could be obtained by applying a low magnetic field. While electrostatics favours side wire interactions due to the high aspect ratio, concurrent electrostatics and applied magnetic field yields end‐to‐end interaction and linear alignment without bifunctionalization. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Effects of electrostatic interactions and geometrical confinements on depletion interactions in charged colloidal system

In a charged colloidal system, the influence on depletion interaction between two like-charged macro-ions is studied through Monte Carlo simulation in this paper. The numerical results show that this depletion force is affected by both the electrostatic interactions between charged spheres and charged plates and by the geometrical factor of the two charged plates, and they further indicate that the influence of geometrical confinement on the depletion interaction is larger than that of electrostatic potential.     

Work and energy in electrostatic and magnetic systems

The equations of motion are obtained for closed systems of charged particles interacting with either an electric or a magnetic field. In each case they include constraints, expressed by the laws of induction, which are of importance in giving a complete specification of the systems usually treated in thermal physics. There are equivalent alternative formulations of the equations of motion, which permit designation of different subsystems; a discussion of these subsystems, their interrelationship, and their external parameters clarifies the significance and applicability of the various expressions for electrical and magnetic work that appear in the general literature. Quantum mechanical treatment of particular subsystems provides a basis for application of statistical mechanics, leading to the identification of appropriate thermodynamic potentials.     

Long time molecular dynamics for enhanced conformational sampling in biomolecular systems

Although molecular dynamics methods are commonly used to drive biomolecular simulations, the technique provides insufficient sampling to impact studies of the 200-300 residue proteins of greatest interest. One severe limitation of molecular dynamics is that the integrators are restricted by resonance phenomena to small time steps (Delta t<8 fs) much slower then the time scales of important structural and solvent rearrangements. Here, a novel set of equations of motion and a reversible, resonance-free, integrator are designed which permit step sizes on the order of 100 fs to be used.     

Parity violation effects of weak interactions on the origin of biomolecular chirality

Summary The process through which the extremely weak parity violation interaction can become the selector of biomolecular chirality via beta-radiolysis over a timet=1500 y is proposed. The mechanism is discussed by using realistic values of the rate constants.

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Riassunto Si dimostra che l'interazione debole avrebbe indotto l'attuale chiralità delle molecole biologiche. Il meccanismo proposto è quello della radiolisi. Usando opportuni valori dei parametri cinetici, l'arco temperale del fenomeno è stimato in 1500 anni.

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Резюме Предлагается процесс, с помощью которого чрезвычайно слабое взаимодействие с нарушением четности может стать селектором биомолекулярной киральности через бета-радиолиз в течениеt=1500 лет. Обсуждается предложенный механизм, используя реалистические значения для постоянных взаимодействия.

     

Real-time and label-free detection of biomolecular interactions by oblique-incidence reflectivity difference method

We successfully conduct the label-free and real-time detection of the interactions between epoxy groups and rabbit IgG and 5' CTT CAG GTC ATG AGC CTG AT 3' oligonucleotide, and between the hybridization of 5' CTT CAG GTC ATG AGC CTG AT 3' and its complementary 3' GAA GTC CAG TAC TCG GAC TA 5' oligonucleotide, by the oblique-incidence reflectivity difference (OI-RD) method. The dynamic curves of OI-RD signals, corresponding to the kinetic processes of biomolecular combination or hybridization, are acquired. In our case, the combination of epoxy groups with rabbit IgG and 5' CTT CAG GTC ATG AGC CTG AT 3' oligonucleotide need almost one and a half hours and about two hundred seconds, respectively; and the hybridization of the two oligonucleotides needs about five hundred seconds. The experimental results show that the OI-RD is a promising method for the real-time and label-free detection of biomolecular interactions.