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B. I. Shklovskii

Publications and source records attributed to B. I. Shklovskii.

At least 91 records · Page 5Linked to original sources

Electrostatic theory of viral self-assembly: a toy model

Viruses self-assemble from identical capsid proteins and their genome consisting, for example, of a long single stranded (ss) RNA. For a big class of T = 3 viruses capsid proteins have long positive N-terminal tails. We explore the role played by the Coulomb interaction between the brush of positive N-terminal tails rooted at the inner surface of the capsid and the negative ss RNA molecule. We show that viruses are most stable when the total contour length of ss RNA is close to the total length of the tails. For such a structure the absolute value of the total RNA charge is approximately twice larger than the charge of the capsid. This conclusion agrees with structural data.

q-bio.BM↗

Kinetics of viral self-assembly: the role of ss RNA antenna

A big class of viruses self-assemble from a large number of identical capsid proteins with long flexible N-terminal tails and ss RNA. We study the role of the strong Coulomb interaction of positive N-terminal tails with ss RNA in the kinetics of the in vitro virus self-assembly. Capsid proteins stick to unassembled chain of ss RNA (which we call "antenna") and slide on it towards the assembly site. We show that at excess of capsid proteins such one-dimensional diffusion accelerates self-assembly more than ten times. On the other hand at excess of ss RNA, antenna slows self-assembly down. Several experiments are proposed to verify the role of ss RNA antenna.

q-bio.BM↗

Hopping conductivity of a suspension of flexible wires in an insulator

We study the hopping conductivity in a composite made of Gaussian coils of flexible metallic wires randomly and isotropically suspended in an insulator at such concentrations that the spheres containing each wire overlap. Uncontrolled donors and acceptors in the insulator lead to random charging of wires and, hence, to a finite density of states (DOS) at the Fermi level. Then the Coulomb interactions between electrons of distant wires result in the soft Coulomb gap. At low temperatures the conductivity is due to variable range hopping of electrons between wires and obeys the Efros-Shklovskii (ES) law $\lnσ\propto -(T_{ES}/T)^{1/2}$ with $T_{ES}$ decreasing with concentration and length of the wires. Due to enhanced screening of Coulomb potentials, at large enough wire concentrations and sufficiently high temperatures, the ES law is replaced by the Mott law $\lnσ\propto -(T_{M}/T)^{1/4}$.

cond-mat.dis-nn↗

Hopping conductivity of a suspension of nanowires in an insulator

We study the hopping conduction in a composite made of straight metallic nanowires randomly and isotropically suspended in an insulator. Uncontrolled donors and acceptors in the insulator lead to random charging of wires and hence finite bare density of states at the Fermi level. Then the Coulomb interactions between electrons of distant wires result in the soft Coulomb gap. At low temperatures the conductivity is due to variable range hopping of electrons between wires and obeys the Efros-Shklovskii (ES) law $\lnσ\propto -(T_{ES}/T)^{1/2}$. We show that $T_{ES} \propto 1/(nL^3)^2$, where $n$ is the concentration of wires and $L$ is the wire length. Due to enhanced screening of Coulomb potentials, at large enough $nL^3$, the ES law is replaced by the Mott law.

cond-mat.dis-nn↗

How does a protein search for the specific site on DNA: the role of disorder

Proteins can locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski three-dimensional diffusion rate. This happens due to non-specific adsorption of proteins to DNA and subsequent one-dimensional sliding along DNA. We call such one-dimensional route towards the target "antenna". We studied the role of the dispersion of nonspecific binding energies within the antenna due to quasi random sequence of natural DNA. Random energy profile for sliding proteins slows the searching rate for the target. We show that this slowdown is different for the macroscopic and mesoscopic antennas.

cond-mat.soft↗

Conductivity of a suspension of nanowires in a weakly conducting medium

We study macroscopic electrical or thermal conductivity of a composite made of straight or coiled nanowires suspended in poorly conducting medium. We assume that volume fraction of the wires is so large that spaces occupied by them overlap, but there is still enough room to distribute wires isotropically. We found a wealth of scaling regimes at different ratios of conductivities of the wire, $σ_1$ and of the medium, $σ_2$, length of wires, their persistent length and volume fraction. There are large ranges of parameters where macroscopic conductivity is proportional to $(σ_{1}σ_{2})^{1/2}$. These results are directly applicable to the calculation of the macroscopic diffusion constant of the nonspecific DNA-binding proteins in semidilute DNA solution.

cond-mat.soft↗

Dyakonov-Perel spin relaxation near metal-insulator transition and in hopping transport

In a heavily doped semiconductor with weak spin-orbital interaction the Dyakonov-Perel spin relaxation rate is known to be proportional to the Drude conductivity. We argue that in the case of weak spin-orbital interaction this proportionality goes beyond the Drude mechanism: it stays valid through the metal-insulator transition and in the range of the exponentially small hopping conductivity.

cond-mat.mes-hall↗

How do proteins search for their specific sites on coiled or globular DNA

It is known since the early days of molecular biology that proteins locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski 3D diffusion rate. It was the idea due to Delbruck that they are non-specifically adsorbed on DNA, and sliding along DNA provides for the faster 1D search. Surprisingly, the role of DNA conformation was never considered in this context. In this article, we explicitly address the relative role of 3D diffusion and 1D sliding along coiled or globular DNA and the possibility of correlated re-adsorbtion of desorbed proteins. We have identified a wealth of new different scaling regimes. We also found the maximal possible acceleration of the reaction due to sliding, we found that the maximum on the rate-versus-ionic strength curve is asymmetric, and that sliding can lead not only to acceleration, but in some regimes to dramatic deceleration of the reaction.

q-bio.BM↗

Ion exchange phase transitions in "doped" water--filled channels

Ion transport through narrow water--filled channels is impeded by a high electrostatic barrier. The latter originates from the large ratio of the dielectric constants of the water and a surrounding media. We show that ``doping'', i.e. immobile charges attached to the walls of the channel, substantially reduces the barrier. This explains why most of the biological ion channels are ``doped''. We show that at rather generic conditions the channels may undergo ion exchange phase transitions (typically of the first order). Upon such a transition a finite latent concentration of ions may either enter or leave the channel, or be exchanged between the ions of different valences. We discuss possible implications of these transitions for the Ca-vs.-Na selectivity of biological Ca channels. We also show that transport of divalent Ca ions is assisted by their fractionalization into two separate excitations.

cond-mat.soft↗

Conductance of ion channels and nanopores with charged walls: a toy model

We consider ion transport through protein ion channels in lipid membranes and water-filled nanopores in silicon films. It is known that, due to the large ratio of dielectric constants of water and the surrounding material, an ion placed inside the channel faces a large electrostatic self-energy barrier. The barrier leads to an exponentially large resistance of the channel. We study reduction of the electrostatic barrier by immobile charges located on the internal walls of the channel. We show that the barrier practically vanishes already at relatively small concentration of wall charges.

cond-mat.soft↗

Transport in one dimensional Coulomb gases: From ion channels to nanopores

We consider a class of systems where, due to the large mismatch of dielectric constants, the Coulomb interaction is approximately one-dimensional. Examples include ion channels in lipid membranes and water filled nanopores in silicon or cellulose acetate films. Charge transport across such systems possesses the activation behavior associated with the large electrostatic self-energy of a charge placed inside the channel. We show here that the activation barrier exhibits non-trivial dependence on the salt concentration in the surrounding water solution and on the length and radius of the channel.

cond-mat.stat-mech↗

Long range polarization attraction between two different likely charged macroions

It is known that in a water solution with multivalent counterions (Z-ions), two likely charged macroions can attract each other due to correlations of Z-ions adsorbed on their surfaces. This "correlation" attraction is short-ranged and decays exponentially with increasing distance between macroions at characteristic distance A/2π, where A is the average distance between Z-ions on the surfaces of macroions. In this work, we show that an additional long range "polarization" attraction exists when the bare surface charge densities of the two macroions have the same sign, but are different in absolute values. The key idea is that with adsorbed Z-ions, two insulating macroions can be considered as conductors with fixed but different electric potentials. Each potential is determined by the difference between the entropic bulk chemical potential of a Z-ion and its correlation chemical potential at the surface of the macroion determined by its bare surface charge density. When the two macroions are close enough, they get polarized in such a way that their adjacent spots form a charged capacitor, which leads to attraction. In a salt free solution this polarization attractive force is long ranged: it decays as a power of the distance between the surfaces of two macroions, d. The polarization force decays slower than the van der Waals attraction and therefore is much larger than it in a large range of distances. In the presence of large amount of monovalent salt, when A/2π<< d<< r_s (r_s is the Debye-Hückel screening radius), this force is still much stronger than the van der Waals attraction and the correlation attraction mentioned above.

cond-mat.soft↗

The pulling force of a single DNA molecule condensed by spermidine

In a recent experiment, a single DNA double helix is stretched and relaxed in the presence of spermidine, a short positive polyelectrolyte, and the pulling force is measured as a function of DNA extension. In a certain range of spermidine concentration, a force plateau appears whose value shows maximum as a function of spermidine concentration. We present a quantitative theory of this plateau force based on the theory of reentrant condensation and derive almost parabolic behavior of the plateau force as a function of the logarithm of the spermidine concentration in the range of condensation. Our result is in good agreement with experimental data.

cond-mat.soft↗

Phase diagram of aggregation of oppositely charged colloids in salty water

Aggregation of two oppositely charged colloids in salty water is studied. We focus on the role of Coulomb interaction in strongly asymmetric systems in which the charge and size of one colloid is much larger than the other one. In the solution, each large colloid (macroion) attracts certain number of oppositely charged small colloids ($Z$-ion) to form a complex. If the concentration ratio of the two colloids is such that complexes are not strongly charged, they condense in a macroscopic aggregate. As a result, the phase diagram in a plane of concentrations of two colloids consists of an aggregation domain sandwiched between two domains of stable solutions of complexes. The aggregation domain has a central part of total aggregation and two wings corresponding to partial aggregation. A quantitative theory of the phase diagram in the presence of monovalent salt is developed. It is shown that as the Debye-Hückel screening radius $r_s$ decreases, the aggregation domain grows, but the relative size of the partial aggregation domains becomes much smaller. As an important application of the theory, we consider solutions of long double-helix DNA with strongly charged positive spheres (artificial chromatin). We also consider implications of our theory for in vitro experiments with the natural chromatin. Finally, the effect of different shapes of macroions on the phase diagram is discussed.

cond-mat.soft↗

Variable-range hopping in quasi-one-dimensional electron crystals

We study the effect of impurities on the ground state and the low-temperature dc transport in a 1D chain and quasi-1D systems of many parallel chains. We assume that strong interactions impose a short-range periodicicity of the electron positions. The long-range order of such an electron crystal (or equivalently, a $4 k_F$ charge-density wave) is destroyed by impurities. The 3D array of chains behaves differently at large and at small impurity concentrations $N$. At large $N$, impurities divide the chains into metallic rods. The low-temperature conductivity is due to the variable-range hopping of electrons between the rods. It obeys the Efros-Shklovskii (ES) law and increases exponentially as $N$ decreases. When $N$ is small, the metallic-rod picture of the ground state survives only in the form of rare clusters of atypically short rods. They are the source of low-energy charge excitations. In the bulk the charge excitations are gapped and the electron crystal is pinned collectively. A strongly anisotropic screening of the Coulomb potential produces an unconventional linear in energy Coulomb gap and a new law of the variable-range hopping $-\lnσ\sim (T_1 / T)^{2/5}$. $T_1$ remains constant over a finite range of impurity concentrations. At smaller $N$ the 2/5-law is replaced by the Mott law, where the conductivity gets suppressed as $N$ goes down. Thus, the overall dependence of $σ$ on $N$ is nonmonotonic. In 1D, the granular-rod picture and the ES apply at all $N$. The conductivity decreases exponentially with $N$. Our theory provides a qualitative explanation for the transport in organic charge-density wave compounds.

cond-mat.mes-hall↗

Coulomb gap and variable range hopping in a pinned Wigner crystal

It is shown that pinning of an electron Wigner crystal by a small concentration of charged impurities creates the finite density of charged localized states near the Fermi level. In the case of residual impurities in the spacer this density of states is related to nonlinear screening of a close acceptor by a Wigner crystal vacancy. On the other hand, intentional doping by a remote layer of donors is a source of a long range potential, which generates dislocations in Wigner crystal. Dislocations in turn create charged localized states near the Fermi level. In both cases Coulomb interaction of localized states leads to the soft Coulomb gap and ES variable range hopping at low enough temperatures.

cond-mat↗

$1/f$ noise in variable range hopping conduction

A mechanism of $1/f$ noise due to traps formed by impurities which have no neighbors with close energies in their vicinity is studied. Such traps slowly exchange electrons with the rest of conducting media. The concentration of traps and proportional to it $1/f$ noise exponentially grow with decreasing temperature in the variable range hopping regime. This theory provides smooth transition to the nearest neighbor hopping case where it predicts a very weak temperature dependence.

cond-mat↗