791 research outputs found
Swollen-Collapsed Transition in Random Hetero-Polymers
A lattice model of a hetero-polymer with random hydrophilic-hydrophobic
charges interacting with the solvent is introduced, whose continnuum
counterpart has been proposed by T. Garel, L. Leibler and H. Orland {J. Phys.
II France 4, 2139 (1994)]. The transfer matrix technique is used to study
various constrained annealed systems which approximate at various degrees of
accuracy the original quenched model. For highly hydrophobic chains an ordinary
-point transition is found from a high temperature swollen phase to a
low temperature compact phase. Depending on the type of constrained averages,
at very low temperatures a swollen phase or a coexistence between compact and
swollen phases are found. The results are carefully compared with the
corresponding ones obtained in the continuum limit, and various improvements in
the original calculations are discussed.Comment: 13 pages, 8 figures; revised version with minor changes, accepted for
publication in European Physical Journal
Cluster Derivation of the Parisi Scheme for Disordered Systems
We propose a general quantitative scheme in which systems are given the
freedom to sacrifice energy equi-partitioning on the relevant time-scales of
observation, and have phase transitions by separating autonomously into ergodic
sub-systems (clusters) with different characteristic time-scales and
temperatures. The details of the break-up follow uniquely from the requirement
of zero entropy for the slower cluster. Complex systems, such as the
Sherrington-Kirkpatrick model, are found to minimise their free energy by
spontaneously decomposing into a hierarchy of ergodically equilibrating degrees
of freedom at different (effective) temperatures. This leads exactly and
uniquely to Parisi's replica symmetry breaking scheme. Our approach, which is
somewhat akin to an earlier one by Sompolinsky, gives new insight into the
physical interpretation of the Parisi scheme and its relations with other
approaches, numerical experiments, and short range models. Furthermore, our
approach shows that the Parisi scheme can be derived quantitatively and
uniquely from plausible physical principles.Comment: 6 pages, 3 figures, proceedings of international conference on
"Disordered And Complex Systems", 10-14 July 2000 King's College Londo
Solvable Lattice Gas Models of Random Heteropolymers at Finite Density: II. Dynamics and Transitions to Compact States
In this paper we analyse both the dynamics and the high density physics of
the infinite dimensional lattice gas model for random heteropolymers recently
introduced in \cite{jort}. Restricting ourselves to site-disordered
heteropolymers, we derive exact closed deterministic evolution equations for a
suitable set of dynamic order parameters (in the thermodynamic limit), and use
these to study the dynamics of the system for different choices of the monomer
polarity parameters. We also study the equilibrium properties of the system in
the high density limit, which leads to a phase diagram exhibiting transitions
between swollen states, compact states, and regions with partial
compactification. Our results find excellent verification in numerical
simulations, and have a natural and appealing interpretation in terms of real
heteropolymers.Comment: 12 pages, 8 eps figures, revised version (to be published in EPJ
Magnetization enumerator of real-valued symmetric channels in Gallager error-correcting codes
Using the magnetization enumerator method, we evaluate the practical and
theoretical limitations of symmetric channels with real outputs. Results are
presented for several regular Gallager code constructions.Comment: 5 pages, 1 figure, to appear as Brief Report in Physical Review
Dependence of endothelial cell growth on substrate-bound fibronectin
A better understanding of the mechanism of adhesion, spreading and proliferation of human endothelial cells (HEC) on polymeric surfaces may lead to the development of vascular prostheses which allow the formation of an endothelial lining on the luminal surface. In the present investigation the interaction of HEC with polyethylene precoated with monoclonal antibodies directed against HEC membrane antigens and against extracellular matrix compounds was studied. F(abÂż)2 fragments of a monoclonal antibody, directed against an endothelial cell membrane antigen, and F(ab')2 fragments of a monoclonal antibody, directed against cellular fibronectin, were also included in this study. Preadsorption of these antibodies and F(ab')2 fragments, including mixtures of antibodies and mixtures of F(ab')2 fragments, resulted in cell adhesion and spreading as well as moderate cell proliferation (or no proliferation) for several days. However, a good proliferation of HEC was only observed on polyethylene precoated with fibronectin or CLB-HEC-FN-140 (directed against fibronectin). These results strongly suggest that fibronectin, bound to a solid substrate, provides a biochemical signal necessary for the proliferation of HEC. The initial proliferation of HEC on other preadsorbed antibodies or F(ab')2 fragments may be explained by the fact that suspended HEC, used for cell seeding, still possess cell membrane-bound fibronectin
The role of cellular fibronectin in the interaction of human endothelial cells with polymers
During in-vitro adhesion, spreading and proliferation of human endothelial cells (HEC) on tissue culture polystyrene (TCPS), cellular fibronectin is deposited onto the surface of TCPS in spite of the fact that relatively large amounts of proteins have been adsorbed from the serum-containing culture medium to this surface. Evidence is presented that serum proteins, adsorbed to the TCPS surface, are displaced by cellular fibronectin. In addition, the interaction of HEC with polyethylene, precoated with monoclonal antibodies directed against HEC membrane antigens and against extracellular matrix compounds, was studied. F(ab')2 fragments of two monoclonal antibodies were also included in this study. Preadsorption of these antibodies and F(ab')2 fragments resulted in cell adhesion and spreading as well as moderate cell proliferation (or no proliferation) for several days. A good cell proliferation of HEC was only observed on polyethylene precoated with fibronectin or an antibody directed against fibronectin. The results indicate that the direct or indirect deposition of fibronectin is a prerequisite for the proliferation of HEC. It is suggested that fibronectin, bound to a solid substrate, provides a biochemical signal necessary for the proliferation of HEC
A Solvable Model of Secondary Structure Formation in Random Hetero-Polymers
We propose and solve a simple model describing secondary structure formation
in random hetero-polymers. It describes monomers with a combination of
one-dimensional short-range interactions (representing steric forces and
hydrogen bonds) and infinite range interactions (representing polarity forces).
We solve our model using a combination of mean field and random field
techniques, leading to phase diagrams exhibiting second-order transitions
between folded, partially folded and unfolded states, including regions where
folding depends on initial conditions. Our theoretical results, which are in
excellent agreement with numerical simulations, lead to an appealing physical
picture of the folding process: the polarity forces drive the transition to a
collapsed state, the steric forces introduce monomer specificity, and the
hydrogen bonds stabilise the conformation by damping the frustration-induced
multiplicity of states.Comment: 24 pages, 14 figure
Survey propagation for the cascading Sourlas code
We investigate how insights from statistical physics, namely survey
propagation, can improve decoding of a particular class of sparse error
correcting codes. We show that a recently proposed algorithm, time averaged
belief propagation, is in fact intimately linked to a specific survey
propagation for which Parisi's replica symmetry breaking parameter is set to
zero, and that the latter is always superior to belief propagation in the high
connectivity limit. We briefly look at further improvements available by going
to the second level of replica symmetry breaking.Comment: 14 pages, 5 figure
Cluster derivation of Parisi's RSB solution for disordered systems
We propose a general scheme in which disordered systems are allowed to
sacrifice energy equi-partitioning and separate into a hierarchy of ergodic
sub-systems (clusters) with different characteristic time-scales and
temperatures. The details of the break-up follow from the requirement of
stationarity of the entropy of the slower cluster, at every level in the
hierarchy. We apply our ideas to the Sherrington-Kirkpatrick model, and show
how the Parisi solution can be {\it derived} quantitatively from plausible
physical principles. Our approach gives new insight into the physics behind
Parisi's solution and its relations with other theories, numerical experiments,
and short range models.Comment: 7 pages 5 figure
Palaeoecological study of a Weichselian wetland site in the Netherlands suggests a link with Dansgaard-Oeschger climate oscillation
Botanical microfossils, macroremains and oribatid mites of a Weichselian interstadial deposit in the central Netherlands point to a temporary, sub-arctic wetland in a treeless landscape. Radiocarbon dates and OSL dates show an age between ca. 54.6 and 46.6 ka cal BP. The vegetation succession, starting as a peat-forming wetland that developed into a lake, might well be linked with a Dansgaard-Oeschger climatic cycle. We suggest that during the rapid warming at the start of a D-O cycle, relatively low areas in the landscape became wetlands where peat was formed. During the more gradual temperature decline that followed, evaporation diminished; the wetlands became inundated and lake sediments were formed. During subsequent sub-arctic conditions the interstadial deposits were covered with wind-blown sand. Apart from changes in effective precipitation also the climate-related presence and absence of permafrost conditions may have played a role in the formation of the observed sedimentological sequence from sand to peat, through lacustrine sediment, with coversand on top. The Wageningen sequence may correspond with D-O event 12, 13 or 14. Some hitherto not recorded microfossils were described and illustrated
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