Search results for "Biomolecules"
showing 10 items of 549 documents
Making Floryr–Huggins Practical: Thermodynamics of Polymer-Containing Mixtures
2010
The theoretical part of this article demonstrates how the original Flory–Huggins theory can be extended to describe the thermodynamic behavior of polymer-containing mixtures quantitatively. This progress is achieved by accounting for two features of macromolecules that the original approach ignores: the effects of chain connectivity in the case of dilute solutions, and the ability of polymer coils to change their spatial extension in response to alterations in their molecular environment. In the general case, this approach leads to composition-dependent interaction parameters, which can for most binary systems be described by means of two physically meaningful parameters; systems involving …
Solubility of Polymers
2011
Detailed knowledge concerning the phase state (homogeneous or coexistence of two or more condensed phases) of polymer containing mixtures is indispensible in virtually any area related to the production or application of macromolecules. In addition to this qualitative information it is for many purposes highly desirable to dispose of quantitative data regarding solvent quality or, more generally, with respect to the thermodynamic interaction between the components of the mixtures. This contribution starts with a brief presentation of the thermodynamic criteria deciding on the phase state and presents the experimental methods used in this area. The next section gives an overview on typical b…
Entropy of glassy polymer melts: Comparison between Gibbs-DiMarzio theory and simulation.
1996
We calculate the free energy of a model for a polymer melt in a computer simulation of the bond-fluctuation model and determine the entropy of the melt over a wide range of temperatures, including the region close to the glass transition. The results are compared with the Gibbs-DiMarzio theory, a theory by Flory for semiflexible polymers, and a modification of their theories due to Milchev. We can describe the data within the framework of the Flory theory with Milchev's correction and discuss the consequences for the understanding of the glass transition. \textcopyright{} 1996 The American Physical Society.
Computer Simulations and Coarse-Grained Molecular Models Predicting the Equation of State of Polymer Solutions
2010
Monte Carlo and molecular dynamics simulations are, in principle, powerful tools for carrying out the basic task of statistical thermodynamics, namely the prediction of macroscopic properties of matter from suitable models of effective interactions between atoms and molecules. The state of the art of this approach is reviewed, with an emphasis on solutions of rather short polymer chains (such as alkanes) in various solvents. Several methods of constructing coarse-grained models of the simple bead–spring type will be mentioned, using input either from atomistic models (considering polybutadiene as an example) or from experiment. Also, the need to have corresponding coarse-grained models of t…
Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints
1996
A new functional representation of NMR-derived distance constraints, the flexible restraint potential, has been implemented in the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168) for molecular structure generation. In addition, flat-bottomed restraint potentials for representing dihedral angle and vicinal scalar coupling constraints have been introduced into CONGEN. An effective simulated annealing (SA) protocol that combines both weight annealing and temperature annealing is described. Calculations have been performed using ideal simulated NMR constraints, in order to evaluate the use of restrained molecular dynamics (MD) with these target functions as implemented i…
Role of Disorder on the Dynamics of a Nonlinear Model for DNA Thermal Denaturation
1992
The dynamics of thermal denaturation of DNA is a good example in which nonlinearity coexits with disorder. The amplitude of the motions is so high that bonds break and the base sequence is inhomogeneous since it contains the genetic code. Using a simple nonlinear model, we study the role of local inhomogeneities or of extended disorder on the dynamics of the localized excitations and on the denaturation rate by numerical simulations at constrained temperature. Approximate analytical results are obtained for the trapping of the breatherlike excitations by isolated defects and the statistical mechanics of the disordered molecule.
Force probe simulations using a hybrid scheme with virtual sites.
2017
Hybrid simulations, in which a part of the system is treated with atomistic resolution and the remainder is represented on a coarse-grained level, allow for fast sampling while using the accuracy of atomistic force fields. We apply a hybrid scheme to study the mechanical unfolding and refolding of a molecular complex using force probe molecular dynamics (FPMD) simulations. The degrees of freedom of the solvent molecules are treated in a coarse-grained manner while atomistic resolution is retained for the solute. The coupling between the solvent and the solute is provided using virtual sites. We test two different common coarse-graining procedures, the iterative Boltzmann inversion method an…
Benchmark Thermochemistry of the Hydroperoxyl Radical
2004
A theoretical estimation of the enthalpy of formation for the hydroperoxyl radical is presented. These results are based on CCSD(T)/aug-cc-pCV5Z calculations extrapolated to the basis-set limit with additional corrections. Anharmonic vibrational zero-point energies, scalar relativistic, spin -orbit coupling, and diagonal BornOppenheimer corrections are further used to correct the extrapolated term energies, as well as various empirical corrections that account for correlation effects not treated at the CCSD(T) level. We estimate that ¢fH° ) 3.66 ( 0.10 kcal mol -1 (¢fH° ) 2.96 ( 0.10 kcal mol -1 ) using several reaction schemes. Significantly, it appears to be necessary to include effects o…
Molecular-dynamics simulation of a glassy polymer melt: Incoherent scattering function
1999
We report results of molecular-dynamics simulations for a glassy polymer melt consisting of short, linear bead-spring chains. It was shown in previous work that this onset of the glassy slowing down is compatible with the predictions of the mode coupling theory. The physical process of `caging' of a monomer by its spatial neighbors leads to a distinct two step behavior in the particle mean square displacements. In this work we analyze the effects of this caging process on the Rouse description of the melt's dynamics. We show that the Rouse theory is applicable for length and time scales above the typical scales for the caging process. Futhermore, the monomer displacement is compared with si…
"Table 1" of "Measurements of the charge asymmetry in top-quark pair production in the dilepton final state at $\sqrt{s}=8$ TeV with the ATLAS detect…
2017
Unfolded distribution for the inclusive $\Delta|\eta|$ observable in the fiducial volume.