245 research outputs found
Skating on a Film of Air: Drops Impacting on a Surface
Drops impacting on a surface are ubiquitous in our everyday experience. This
impact is understood within a commonly accepted hydrodynamic picture: it is
initiated by a rapid shock and a subsequent ejection of a sheet leading to
beautiful splashing patterns. However, this picture ignores the essential role
of the air that is trapped between the impacting drop and the surface. Here we
describe a new imaging modality that is sensitive to the behavior right at the
surface. We show that a very thin film of air, only a few tens of nanometers
thick, remains trapped between the falling drop and the surface as the drop
spreads. The thin film of air serves to lubricate the drop enabling the fluid
to skate on the air film laterally outward at surprisingly high velocities,
consistent with theoretical predictions. Eventually this thin film of air must
break down as the fluid wets the surface. We suggest that this occurs in a
spinodal-like fashion, and causes a very rapid spreading of a wetting front
outwards; simultaneously the wetting fluid spreads inward much more slowly,
trapping a bubble of air within the drop. Our results show that the dynamics of
impacting drops are much more complex than previously thought and exhibit a
rich array of unexpected phenomena that require rethinking classical paradigms.Comment: 4 pages, 4 figure
Phase Transitions of Single Semi-stiff Polymer Chains
We study numerically a lattice model of semiflexible homopolymers with
nearest neighbor attraction and energetic preference for straight joints
between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched
Rosenbluth Method" (PERM). It is very efficient both for relatively open
configurations at high temperatures and for compact and frozen-in low-T states.
This allows us to study in detail the phase diagram as a function of
nn-attraction epsilon and stiffness x. It shows a theta-collapse line with a
transition from open coils to molten compact globules (large epsilon) and a
freezing transition toward a state with orientational global order (large
stiffness x). Qualitatively this is similar to a recently studied mean field
theory (Doniach et al. (1996), J. Chem. Phys. 105, 1601), but there are
important differences. In contrast to the mean field theory, the
theta-temperature increases with stiffness x. The freezing temperature
increases even faster, and reaches the theta-line at a finite value of x. For
even stiffer chains, the freezing transition takes place directly without the
formation of an intermediate globule state. Although being in contrast with
mean filed theory, the latter has been conjectured already by Doniach et al. on
the basis of low statistics Monte Carlo simulations. Finally, we discuss the
relevance of the present model as a very crude model for protein folding.Comment: 11 pages, Latex, 8 figure
Chirality and Protein Folding
There are several simple criteria of folding to a native state in model
proteins. One of them involves crossing of a threshold value of the RMSD
distance away from the native state. Another checks whether all native contacts
are established, i.e. whether the interacting amino acids come closer than some
characteristic distance. We use Go-like models of proteins and show that such
simple criteria may prompt one to declare folding even though fragments of the
resulting conformations have a wrong sense of chirality. We propose that a
better condition of folding should augment the simple criteria with the
requirement that most of the local values of the chirality should be nearly
native. The kinetic discrepancy between the simple and compound criteria can be
substantially reduced in the Go-like models by providing the Hamiltonian with a
term which favors native values of the local chirality. We study the effects of
this term as a function of its amplitude and compare it to other models such as
with the side groups and with the angle-dependent potentials.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo
Workshop
Topological effects in ring polymers: A computer simulation study
Unconcatenated, unknotted polymer rings in the melt are subject to strong
interactions with neighboring chains due to the presence of topological
constraints. We study this by computer simulation using the bond-fluctuation
algorithm for chains with up to N=512 statistical segments at a volume fraction
\Phi=0.5 and show that rings in the melt are more compact than gaussian chains.
A careful finite size analysis of the average ring size R \propto N^{\nu}
yields an exponent \nu \approx 0.39 \pm 0.03 in agreement with a Flory-like
argument for the topologica interactions. We show (using the same algorithm)
that the dynamics of molten rings is similar to that of linear chains of the
same mass, confirming recent experimental findings. The diffusion constant
varies effectively as D_{N} \propto N^{-1.22(3) and is slightly higher than
that of corresponding linear chains. For the ring sizes considered (up to 256
statistical segments) we find only one characteristic time scale \tau_{ee}
\propto N^{2.0(2); this is shown by the collapse of several mean-square
displacements and correlation functions onto corresponding master curves.
Because of the shrunken state of the chain, this scaling is not compatible with
simple Rouse motion. It applies for all sizes of ring studied and no sign of a
crossover to any entangled regime is found.Comment: 20 Pages,11 eps figures, Late
A refined hydrogen bond potential for flexible protein models
One of the major disadvantages of coarse-grained hydrogen bond potentials, for their use in protein folding simulations, is the appearance of abnormal structures when these potentials are used in flexible chain models, and no other geometrical restrictions or energetic contributions are defined into the system.We have efficiently overcome this problem, for chains of adequate size in a relevant temperature range, with a refined coarse-grained hydrogen bond potential. With it, we have been able to obtain nativelike alpha-helices and beta-sheets in peptidic systems, and successfully reproduced the competition between the populations of these secondary structure elements by the effect of temperature and concentration changes. In this manuscript we detail the design of the interaction potential and thoroughly examine its applicability in energetic and structural terms, considering factors such as chain length, concentration, and temperature
Simulating chemistry using quantum computers
The difficulty of simulating quantum systems, well-known to quantum chemists,
prompted the idea of quantum computation. One can avoid the steep scaling
associated with the exact simulation of increasingly large quantum systems on
conventional computers, by mapping the quantum system to another, more
controllable one. In this review, we discuss to what extent the ideas in
quantum computation, now a well-established field, have been applied to
chemical problems. We describe algorithms that achieve significant advantages
for the electronic-structure problem, the simulation of chemical dynamics,
protein folding, and other tasks. Although theory is still ahead of experiment,
we outline recent advances that have led to the first chemical calculations on
small quantum information processors.Comment: 27 pages. Submitted to Ann. Rev. Phys. Che
Three-helix-bundle Protein in a Ramachandran Model
We study the thermodynamic behavior of a model protein with 54 amino acids
that forms a three-helix bundle in its native state. The model contains three
types of amino acids and five to six atoms per amino acid and has the
Ramachandran torsional angles , as its degrees of freedom. The
force field is based on hydrogen bonds and effective hydrophobicity forces. For
a suitable choice of the relative strength of these interactions, we find that
the three-helix-bundle protein undergoes an abrupt folding transition from an
expanded state to the native state. Also shown is that the corresponding one-
and two-helix segments are less stable than the three-helix sequence.Comment: 15 pages, 7 figure
Cooperative Dynamics in Unentangled Polymer Fluids
We present a Generalized Langevin Equation for the dynamics of interacting
semiflexible polymer chains, undergoing slow cooperative dynamics. The
calculated Gaussian intermolecular center-of-mass and monomer potentials, wich
enter the GLE, are in quantitative agreement with computer simulation data. The
experimentally observed, short-time subdiffusive regime of the polymer
mean-square displacements, emerges here from the competition between the
intramolecular and the intermolecular mean-force potentials.Comment: 9 pages, latex, 3 figure
Short Time Behavior in De Gennes' Reptation Model
To establish a standard for the distinction of reptation from other modes of
polymer diffusion, we analytically and numerically study the displacement of
the central bead of a chain diffusing through an ordered obstacle array for
times . Our theory and simulations agree quantitatively and show
that the second moment approaches the often viewed as signature of
reptation only after a very long transient and only for long chains (N > 100).
Our analytically solvable model furthermore predicts a very short transient for
the fourth moment. This is verified by computer experiment.Comment: 4 pages, revtex, 4 ps file
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