1,505 research outputs found
Effect of Interactions on Molecular Fluxes and Fluctuations in the Transport Across Membrane Channels
Transport of molecules across membrane channels is investigated theoretically
using exactly solvable one-dimensional discrete-state stochastic models. An
interaction between molecules and membrane pores is modeled via a set of
binding sites with different energies. It is shown that the interaction
potential strongly influences the particle currents as well as fluctuations in
the number of translocated molecules. For small concentration gradients the
attractive sites lead to largest currents and fluctuations, while the repulsive
interactions yield the largest fluxes and dispersions for large concentration
gradients. Interaction energies that lead to maximal currents and maximal
fluctuations are the same only for locally symmetric potentials, while they
differ for the locally asymmetric potentials. The conditions for the most
optimal translocation transport with maximal current and minimal dispersion are
discussed. It is argued that in this case the interaction strength is
independent of local symmetry of the potential of mean forces. In addition, the
effect of the global asymmetry of the interaction potential is investigated,
and it is shown that it also strongly affects the particle translocation
dynamics. These phenomena can be explained by analyzing the details of the
particle entering and leaving the binding sites in the channel.Comment: submitted to J. Chem. Phy
Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase : dynamics in nucleotides, amino acids and beyond
In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach
Effect of Inhomogeneity in Translocation of Polymers through Nanopores
The motion of polymers with inhomogeneous structure through nanopores is
discussed theoretically. Specifically, we consider the translocation dynamics
of polymers consisting of double-stranded and single-stranded blocks. Since
only the single-stranded chain can go through the nanopore the double-stranded
segment has to unzip before the translocation. Utilizing a simple analytical
model, translocation times are calculated explicitly for different polymer
orientations, i.e., when the single-stranded block enters the pore first and
when the double-stranded segment is a leading one. The dependence of the
translocation dynamics on external fields, energy of interaction in the
double-stranded segment, size of the polymer and the fraction of
double-stranded monomers is analyzed. It is found that the order of entrance
into the pore has a significant effect on the translocation dynamics. The
theoretical results are discussed using free-energy landscape arguments.Comment: 12 pages, 5 figures, submitted to J. Chem. Phy
Numerical simulation of conformational variability in biopolymer translocation through wide nanopores
Numerical results on the translocation of long biopolymers through mid-sized
and wide pores are presented. The simulations are based on a novel methodology
which couples molecular motion to a mesoscopic fluid solvent. Thousands of
events of long polymers (up to 8000 monomers) are monitored as they pass
through nanopores. Comparison between the different pore sizes shows that wide
pores can host a larger number of multiple biopolymer segments, as compared to
smaller pores. The simulations provide clear evidence of folding quantization
in the translocation process as the biopolymers undertake multi-folded
configurations, characterized by a well-defined integer number of folds.
Accordingly, the translocation time is no longer represented by a
single-exponent power law dependence on the length, as it is the case for
single-file translocation through narrow pores. The folding quantization
increases with the biopolymer length, while the rate of translocated beads at
each time step is linearly correlated to the number of resident beads in the
pore. Finally, analysis of the statistics over the translocation work unravels
the importance of the hydrodynamic interactions in the process.Comment: 10 pages, 6 figures, to appear in J. Stat. (2009
Models of dynamic extraction of lipid tethers from cell membranes
When a ligand that is bound to an integral membrane receptor is pulled, the
membrane and the underlying cytoskeleton can deform before either the membrane
delaminates from the cytoskeleton or the ligand detaches from the receptor. If
the membrane delaminates from the cytoskeleton, it may be further extruded and
form a membrane tether. We develop a phenomenological model for this processes
by assuming that deformations obey Hooke's law up to a critical force at which
the cell membrane locally detaches from the cytoskeleton and a membrane tether
forms. We compute the probability of tether formation and show that they can be
extruded only within an intermediate range of force loading rates and pulling
velocities. The mean tether length that arises at the moment of ligand
detachment is computed as are the force loading rates and pulling velocities
that yield the longest tethers.Comment: 16 pages, 7 figure
A novel method for measuring the bending rigidity of model lipid membranes by simulating tethers
The tensile force along a cylindrical lipid bilayer tube is proportional to
the membrane's bending modulus and inversely proportional to the tube radius.
We show that this relation, which is experimentally exploited to measure
bending rigidities, can be applied with even greater ease in computer
simulations. Using a coarse-grained bilayer model we efficiently obtain bending
rigidities that compare very well with complementary measurements based on an
analysis of thermal undulation modes. We furthermore illustrate that no
deviations from simple quadratic continuum theory occur up to a radius of
curvature comparable to the bilayer thickness.Comment: 7 pages, 5 figures, 1 tabl
Protein search for multiple targets on DNA
Protein-DNA interactions are crucial for all biological processes. One of the
most important fundamental aspects of these interactions is the process of
protein searching and recognizing specific binding sites on DNA. A large number
of experimental and theoretical investigations have been devoted to uncovering
the molecular description of these phenomena, but many aspects of the
mechanisms of protein search for the targets on DNA remain not well understood.
One of the most intriguing problems is the role of multiple targets in protein
search dynamics. Using a recently developed theoretical framework we analyze
this question in detail. Our method is based on a discrete-state stochastic
approach that takes into account most relevant physical-chemical processes and
leads to fully analytical description of all dynamic properties. Specifically,
systems with two and three targets have been explicitly investigated. It is
found that multiple targets in most cases accelerate the search in comparison
with a single target situation. However, the acceleration is not always
proportional to the number of targets. Surprisingly, there are even situations
when it takes longer to find one of the multiple targets in comparison with the
single target. It depends on the spatial position of the targets, distances
between them, average scanning lengths of protein molecules on DNA, and the
total DNA lengths. Physical-chemical explanations of observed results are
presented. Our predictions are compared with experimental observations as well
as with results from a continuum theory for the protein search. Extensive Monte
Carlo computer simulations fully support our theoretical calculations
First-principles GW calculations for DNA and RNA nucleobases
On the basis of first-principles GW calculations, we study the quasiparticle
properties of the guanine, adenine, cytosine, thymine, and uracil DNA and RNA
nucleobases. Beyond standard G0W0 calculations, starting from Kohn-Sham
eigenstates obtained with (semi)local functionals, a simple self-consistency on
the eigenvalues allows to obtain vertical ionization energies and electron
affinities within an average 0.11 eV and 0.18 eV error respectively as compared
to state-of-the-art coupled-cluster and multi-configurational perturbative
quantum chemistry approaches. Further, GW calculations predict the correct \pi
-character of the highest occupied state, thanks to several level crossings
between density functional and GW calculations. Our study is based on a recent
gaussian-basis implementation of GW with explicit treatment of dynamical
screening through contour deformation techniques.Comment: 5 pages, 3 figure
Transport of Molecular Motor Dimers in Burnt-Bridge Models
Dynamics of molecular motor dimers, consisting of rigidly bound particles
that move along two parallel lattices and interact with underlying molecular
tracks, is investigated theoretically by analyzing discrete-state stochastic
continuous-time burnt-bridge models. In these models the motion of molecular
motors is viewed as a random walk along the lattices with periodically
distributed weak links (bridges). When the particle crosses the weak link it
can be destroyed with a probability , driving the molecular motor motion in
one direction. Dynamic properties and effective generated forces of dimer
molecular motors are calculated exactly as a function of a concentration of
bridges and burning probability and compared with properties of the
monomer motors. It is found that the ratio of the velocities of the dimer and
the monomer can never exceed 2, while the dispersions of the dimer and the
monomer are not very different. The relative effective generated force of the
dimer (as compared to the monomer) also cannot be larger than 2 for most sets
of parameters. However, a very large force can be produced by the dimer in the
special case of for non-zero shift between the lattices. Our
calculations do not show the significant increase in the force generated by
collagenase motor proteins in real biological systems as predicted by previous
computational studies. The observed behavior of dimer molecular motors is
discussed by considering in detail the particle dynamics near burnt bridges.Comment: 21 pages and 11 figure
Sequence Heterogeneity Accelerates Protein Search for Targets on DNA
The process of protein search for specific binding sites on DNA is
fundamentally important since it marks the beginning of all major biological
processes. We present a theoretical investigation that probes the role of DNA
sequence symmetry, heterogeneity and chemical composition in the protein search
dynamics. Using a discrete-state stochastic approach with a first-passage
events analysis, which takes into account the most relevant physical-chemical
processes, a full analytical description of the search dynamics is obtained. It
is found that, contrary to existing views, the protein search is generally
faster on DNA with more heterogeneous sequences. In addition, the search
dynamics might be affected by the chemical composition near the target site.
The physical origins of these phenomena are discussed. Our results suggest that
biological processes might be effectively regulated by modifying chemical
composition, symmetry and heterogeneity of a genome.Comment: 10 pages, 5 figure
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