Heat conductivity of DNA double helix

Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal conductivity. To investigate thermal properties of single molecule DNA we have developed a 3D coarse-grained (CG) model that retains the realism of the full all-atom description, but is significantly more efficient. Within the proposed model each nucleotide is represented by 6 particles or grains; the grains interact via effective potentials inferred from classical molecular dynamics (MD) trajectories based on a well-established all-atom potential function. Comparisons of 10 ns long MD trajectories between the CG and the corresponding all-atom model show similar root-mean-square deviations from the canonical B-form DNA, and similar structural fluctuations. At the same time, the CG model is 10 to 100 times faster depending on the length of the DNA fragment in the simulation. Analysis of dispersion curves derived from the CG model yields longitudinal sound velocity and torsional stiffness in close agreement with existing experiments. The computational efficiency of the CG model makes it possible to calculate thermal conductivity of a single DNA molecule not yet available experimentally. For a uniform (polyG-polyC) DNA, the estimated conductivity coefficient is 0.3 W/mK which is half the value of thermal conductivity for water. This result is in stark contrast with estimates of thermal conductivity for simplified, effectively 1D chains ("beads on a spring") that predict anomalous (infinite) thermal conductivity. Thus, full 3D character of DNA double-helix retained in the proposed model appears to be essential for describing its thermal properties at a single molecule level.Comment: 16 pages, 12 figure

The role of chromosome-nuclear envelope attachments in 3D genome organization

Chromosomes are intricately folded and packaged in the cell nucleus and interact with the nuclear envelope. This complex nuclear architecture has a profound effect on how the genome works and how the cells function. The main goal of review is to highlight recent studies on the effect of chromosome–nuclear envelope interactions on chromatin folding and function in the nucleus. The data obtained suggest that chromosome–nuclear envelope attachments are important for the organization of nuclear architecture in various organisms. A combination of experimental cell biology methods with computational modeling offers a unique opportunity to explore the fundamental relationships between different aspects of 3D genome organization in greater details. This powerful interdisciplinary approach could reveal how the organization and function of the genome in the nuclear space is affected by the chromosome–nuclear envelope attachments and will enable the development of novel approaches to regulate gene expression

Two-phase stretching of molecular chains

While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension characteristics of the polymer chain with the convexity properties of the extension energy profile of its individual monomer subunits. Namely, if the effective monomer deformation energy as a function of its extension has a non-convex (concave up) region, the stretched polymer chain separates into two phases: the weakly and strongly stretched monomers. Simplified planar and 3D polymer models are used to illustrate the basic principles of the proposed model. Specifically, we show rigorously that when the secondary structure of a polymer is mostly due to weak non-covalent interactions, the stretching is two-phase, and the force-stretching diagram has the characteristic plateau. We then use realistic coarse-grained models to confirm the main findings and make direct connection to the microscopic structure of the monomers. We demostrate in detail how the two-phase scenario is realized in the \alpha-helix, and in DNA double helix. The predicted plateau parameters are consistent with single molecules experiments. Detailed analysis of DNA stretching demonstrates that breaking of Watson-Crick bonds is not necessary for the existence of the plateau, although some of the bonds do break as the double-helix extends at room temperature. The main strengths of the proposed theory are its generality and direct microscopic connection.Comment: 16 pges, 22 figure

Magnetic properties of an SU(4) spin-orbital chain

In this paper, we study the magnetic properties of the one-dimensional SU(4) spin-orbital model by solving its Bethe ansatz solution numerically. It is found that the magnetic properties of the system for the case of $g_t=1.0$ differs from that for the case of $g_t=0.0$. The magnetization curve and susceptibility are obtained for a system of 200 sites. For $0<g_t<g_s$, the phase diagram depending on the magnetic field and the ratio of Land\'e factors, $g_t/g_s$, is obtained. Four phases with distinct magnetic properties are found.Comment: 4 pages, 2 figure

Phase diagram and symmetry breaking of SU(4) spin-orbital chain in a generalized external field

The ground state phases of a one-dimensional SU(4) spin-orbital Hamiltonian in a generalized external field are studied on the basis of Bethe-ansatz solution. Introducing three Land\'e $g$ factors for spin, orbital and their products in the SU(4) Zeeman term, we discuss systematically the various symmetry breaking. The magnetization versus external field are obtained by solving Bethe-ansatz equations numerically. The phase diagrams corresponding to distinct residual symmetries are given by means of both numerical and analytical methods.Comment: Revtex4, 16 pages, 7 figure

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

An extension of the constant pH method originally implemented by Mongan et al. (J. Comput. Chem.2004, 25, 2038−2048) is proposed in this study. This adapted version of the method couples the constant pH methodology with the enhanced sampling technique of accelerated molecular dynamics, in an attempt to overcome the sampling issues encountered with current standard constant pH molecular dynamics methods. Although good results were reported by Mongan et al. on application of the standard method to the hen egg-white lysozyme (HEWL) system, residues which possess strong interactions with neighboring groups tend to converge slowly, resulting in the reported inconsistencies for predicted pKa values, as highlighted by the authors. The application of the coupled method described in this study to the HEWL system displays improvements over the standard version of the method, with the improved sampling leading to faster convergence and producing pKa values in closer agreement to those obtained experimentally for the more slowly converging residues

Integrity of H1 helix in prion protein revealed by molecular dynamic simulations to be especially vulnerable to changes in the relative orientation of H1 and its S1 flank

In the template-assistance model, normal prion protein (PrPC), the pathogenic cause of prion diseases such as Creutzfeldt-Jakob (CJD) in human, Bovine Spongiform Encephalopathy (BSE) in cow, and scrapie in sheep, converts to infectious prion (PrPSc) through an autocatalytic process triggered by a transient interaction between PrPC and PrPSc. Conventional studies suggest the S1-H1-S2 region in PrPC to be the template of S1-S2 $\beta$-sheet in PrPSc, and the conformational conversion of PrPC into PrPSc may involve an unfolding of H1 in PrPC and its refolding into the $\beta$-sheet in PrPSc. Here we conduct a series of simulation experiments to test the idea of transient interaction of the template-assistance model. We find that the integrity of H1 in PrPC is vulnerable to a transient interaction that alters the native dihedral angles at residue Asn$^{143}$, which connects the S1 flank to H1, but not to interactions that alter the internal structure of the S1 flank, nor to those that alter the relative orientation between H1 and the S2 flank.Comment: A major revision on statistical analysis method has been made. The paper now has 23 pages, 11 figures. This work was presented at 2006 APS March meeting session K29.0004 at Baltimore, MD, USA 3/13-17, 2006. This paper has been accepted for pubcliation in European Biophysical Journal on Feb 2, 200

Ground State and Excitations of Spin Chain with Orbital Degeneracy

The one dimensional Heisenberg model in the presence of orbital degeneracy is studied at the SU(4) symmetric viewpoint by means of Bethe ansatz. Following Sutherland's previous work on an equivalent model, we discuss the ground state and the low-lying excitations more extensively in connection to the spin systems with orbital degeneracy. We show explicitly that the ground state is a SU(4) singlet. We study the degeneracies of the elementary excitations and the spectra of the generalized magnons consisting of these excitations. We also discuss the complex 2-strings in the context of the Bethe ansatz solutions.Comment: Revtex, 9 pages, 3 figures; typos correcte

Room Temperature Kondo effect in atom-surface scattering: dynamical 1/N approach

The Kondo effect may be observable in some atom-surface scattering experiments, in particular, those involving alkaline-earth atoms. By combining Keldysh techniques with the NCA approximation to solve the time-dependent Newns-Anderson Hamiltonian in the infinite-U limit, Shao, Nordlander and Langreth found an anomalously strong surface-temperature dependence of the outgoing charge state fractions. Here we employ the dynamical 1/N expansion with finite Coulomb interaction U to provide a more realistic description of the scattering process. We test the accuracy of the 1/N expansion in the spinless N = 1 case against the exact independent-particle solution. We then compare results obtained in the infinite-U limit with the NCA approximation and recover qualitative features found previously. Finally, we analyze the realistic situation of Ca atoms with U = 5.8 eV scattered off Cu(001) surfaces. Although the presence of the doubly-ionized Ca species can change the absolute scattered positive Ca yields, the temperature dependence is qualitatively the same as that found in the infinite-U limit. One of the main difficulties that experimentalists face in attempting to detect this effect is that the atomic velocity must be kept small enough to reduce possible kinematic smearing of the metal's Fermi surface.Comment: 15 pages, 10 Postscript figures; references and typos correcte