Search results for "SIMULATION"
showing 10 items of 5095 documents
Mechanical unfolding pathway of a model β-peptide foldamer.
2015
Foldamers constructed from oligomers of β-peptides form stable secondary helix structures already for small chain lengths, which makes them ideal candidates for the investigation of the (un)folding of polypeptides. Here, the results of molecular simulations of the mechanical unfolding of a β-heptapeptide in methanol solvent revealing the detailed unfolding pathway are reported. The unfolding process is shown to proceed via a stable intermediate even for such a small system. This result is arrived at performing non-equilibrium force ramp simulations employing different pulling velocities and also using standard calculations of the potential of mean force, i.e., the free energy as a function …
Structure and Matrix Isolation Infrared Spectrum of Formyl Fluoride Dimer: Blue-Shift of the C−H Stretching Frequency
2006
Infrared spectroscopy (IR) of formyl fluoride (HCOF) dimer is studied in low-temperature argon and krypton matrixes. New IR absorptions, ca. 17 cm(-1) blue shifted from the monomer C-H stretching fundamental, are assigned to the HCOF dimer. The MP2/6-311++G calculations were utilized to define structures and harmonic frequencies of various HCOF dimers. Among the four optimized structures, the dimer having two C-H...O hydrogen bonds possesses strongest intermolecular bonding. The calculated harmonic frequencies of this dimer structure are shifted from the monomer similarly as observed in the experiment. Thus, we suggest that the experimentally observed blue shifted C-H bands belong to the di…
Conformational Changes of a Single Semiflexible Macromolecule Near an Adsorbing Surface: A Monte Carlo Simulation
2009
The properties of a single semiflexible chain tethered to a planar surface with a long-ranged attractive potential are studied by means of Monte Carlo simulations. We employ the bond fluctuation lattice model and the Wang-Landau sampling technique. We present the diagram of states for semiflexible chains consisting of N = 64 and 128 monomer units as a function of temperature T and strength of the adsorption potential, epsilon(w), and also compare this with the diagram of states for flexible chains of these two lengths. The diagram of states consists of the regions of a coil, liquid globule, solid isotropic globule, adsorbed coil, and quasi-two-dimensional solid globule with nematic bond ord…
Interface and Surface Properties of Short Polymers in Solution: Monte Carlo Simulations and Self-Consistent Field Theory
2000
We investigate the structure and thermodynamics of inhomogeneous polymer solutions in the framework of a coarse-grained off-lattice model. Properties of the liquidvapor interface and the packing of...
An approach to evaluation of sheet bending force under successive multiaxial stress condition
2009
A new bending under tension test is presented in this paper. This method tries to evaluate bending forces in sheet under successive multiaxial stress condition. This test is carried out in only one step with a pinned cylinder over a material that has been previously deformed to pure shear condition. Due to that, the bending process is made under higher back tension forces than the ones involved in the common methods previously studied in the literature. This entails high pressure values in the sheet-bending tool contact that affects the corresponding friction process. Material is strongly strengthened as a consequence of the deformation practiced in it, and as a result of that, bending forc…
Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute
1999
AbstractMolecular dynamics simulations using a simple multielement model solute with internal degrees of freedom and accounting for solvent-induced interactions to all orders in explicit water are reported. The potential energy landscape of the solute is flat in vacuo. However, the sole untruncated solvent-induced interactions between apolar (hydrophobic) and charged elements generate a rich landscape of potential of mean force exhibiting typical features of protein landscapes. Despite the simplicity of our solute, the depth of minima in this landscape is not far in size from free energies that stabilize protein conformations. Dynamical coupling between configurational switching of the syst…
Periodic orbits of single neuron models with internal decay rate 0 < β ≤ 1
2013
In this paper we consider a discrete dynamical system x n+1=βx n – g(x n ), n=0,1,..., arising as a discrete-time network of a single neuron, where 0 < β ≤ 1 is an internal decay rate, g is a signal function. A great deal of work has been done when the signal function is a sigmoid function. However, a signal function of McCulloch-Pitts nonlinearity described with a piecewise constant function is also useful in the modelling of neural networks. We investigate a more complicated step signal function (function that is similar to the sigmoid function) and we will prove some results about the periodicity of solutions of the considered difference equation. These results show the complexity of …
Power-law hereditariness of hierarchical fractal bones
2013
SUMMARY In this paper, the authors introduce a hierarchic fractal model to describe bone hereditariness. Indeed, experimental data of stress relaxation or creep functions obtained by compressive/tensile tests have been proved to be fit by power law with real exponent 0 ⩽ β ⩽1. The rheological behavior of the material has therefore been obtained, using the Boltzmann–Volterra superposition principle, in terms of real order integrals and derivatives (fractional-order calculus). It is shown that the power laws describing creep/relaxation of bone tissue may be obtained by introducing a fractal description of bone cross-section, and the Hausdorff dimension of the fractal geometry is then related …
A theoretical approach of the propagation through geometrical constraints in cardiac tissue
2007
International audience; The behaviour of impulse propagation in the presence of non-excitable scars and boundaries is a complex phenomenon and induces pathological consequences in cardiac tissue. In this article, a geometrical con¯guration is considered so that cardiac waves propagate through a thin strand, which is connected to a large mass of cells. At this interface, waves can slow down or even be blocked depending on the width of the strand. We present an analytical approach leading to determine the blockade condition, by introducing planar travelling wavefront and circular stationary wave. Eventually, the in°uence of the tissue geometry is examined on the impulse propagation velocity.
In silico molecular investigations of pyridine N-Oxide compounds as potential inhibitors of SARS-CoV-2: 3D QSAR, molecular docking modeling, and ADME…
2020
The new coronavirus SARS-CoV-2 virus is causing a severe pneumonia in human, provoking the serious outbreak epidemic CoV-2. Since its appearance in Wuhan, China on December 2019, CoV-2 becomes the biggest challenge the world is facing today, including the discovery of antiviral drug for SARS-CoV-2. In this study, the potential inhibitory of a class of human SARS inhibitors, namely pyridine N-oxide derivatives, against CoV-2 was addressed by quantitative structure-activity relationship 3 D-QSAR. The reliable CoMSIA developed model of 110 pyridine N-oxide based-antiviral compounds, showed Q