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Area per lipid and acyl length distributions in fluid phosphatidylcholines determined by 2H NMR spectroscopy, Biophys
 J
"... ABSTRACT Deuterium (2H) NMR spectroscopy provides detailed information regarding the structural fluctuations of lipid bilayers, including both the equilibrium properties and dynamics. Experimental 2H NMR measurements for the homologous series of 1,2diacylsnglycero3phosphocholines with perdeuter ..."
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Cited by 52 (6 self)
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ABSTRACT Deuterium (2H) NMR spectroscopy provides detailed information regarding the structural fluctuations of lipid bilayers, including both the equilibrium properties and dynamics. Experimental 2H NMR measurements for the homologous series of 1,2diacylsnglycero3phosphocholines with perdeuterated saturated chains (from C12:0 to C18:0) have been performed on randomly oriented, fully hydrated multilamellar samples. For each lipid, the C–D bond order parameters have been calculated from dePaked 2H NMR spectra as a function of temperature. The experimental order parameters were analyzed using a meantorque potential model for the acyl chain segment distributions, and comparison was made with the conventional diamond lattice approach. Statistical mechanical principles were used to relate the measured order parameters to the lipid bilayer structural parameters: the hydrocarbon thickness and the mean interfacial area per lipid. At fixed temperature, the area decreases with increasing acyl length, indicating increased van der Waals attraction for longer lipid chains. However, the main effect of increasing the acyl chain length is on the hydrocarbon thickness rather than on the area per lipid. Expansion coefficients of the structural parameters are reported and interpreted using an empirical free energy function that describes the force balance in fluid bilayers. At the same absolute temperature, the phosphatidylcholine (PC) series exhibits a universal chain packing profile that differs from that of phosphatidylethanolamines (PE). Hence, the lateral packing of phospholipids is more sensitive to the headgroup methylation than to the acyl chain length. A fit to the area per lipid for the PC series using the empirical free energy function shows that the PE area represents a limiting value for the packing of fluid acyl chains.
Barrelstave model or toroidal model? A case study on melittin pores. Biophys
, 2001
"... ABSTRACT Transmembrane pores induced by amphiphilic peptides, including melittin, are often modeled with the barrelstave model after the alamethicin pore. We examine this assumption on melittin by using two methods, oriented circular dichroism (OCD) for detecting the orientation of melittin helix an ..."
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Cited by 47 (3 self)
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ABSTRACT Transmembrane pores induced by amphiphilic peptides, including melittin, are often modeled with the barrelstave model after the alamethicin pore. We examine this assumption on melittin by using two methods, oriented circular dichroism (OCD) for detecting the orientation of melittin helix and neutron scattering for detecting transmembrane pores. OCD spectra of melittin were systematically measured. Melittin can orient either perpendicularly or parallel to a lipid bilayer, depending on the physical condition and the composition of the bilayer. Transmembrane pores were detected when the helices oriented perpendicularly to the plane of the bilayers, not when the helices oriented parallel to the bilayers. The evidence that led to the barrelstave model for alamethicin and that to the toroidal model for magainin were reviewed. The properties of melittin pores are closely similar to that of magainin but unlike that of alamethicin. We conclude that, among naturally produced peptides that we have investigated, only alamethicin conforms to the barrelstave model. Other peptides, including magainins, melittin and protegrins, all appear to induce transmembrane pores that conform to the toroidal model in which the lipid monolayer bends continuously through the pore so that the water core is lined by both the peptides and the lipid headgroups.
H.: The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
 The Journal of Physical Chemistry B
"... We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To rep ..."
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Cited by 44 (4 self)
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We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarsegrained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations. 1.
Convergence of peridynamics to classical elasticity theory
 Journal of Elasticity
"... Abstract The peridynamic model of solid mechanics is a nonlocal theory containing a length scale. It is based on direct interactions between points in a continuum separated from each other by a finite distance. The maximum interaction distance provides a length scale for the material model. This pap ..."
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Cited by 30 (5 self)
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Abstract The peridynamic model of solid mechanics is a nonlocal theory containing a length scale. It is based on direct interactions between points in a continuum separated from each other by a finite distance. The maximum interaction distance provides a length scale for the material model. This paper addresses the question of whether the peridynamic model for an elastic material reproduces the classical local model as this length scale goes to zero. We show that if the motion, constitutive model, and any nonhomogeneities are sufficiently smooth, then the peridynamic stress tensor converges in this limit to a PiolaKirchhoff stress tensor that is a function only of the local deformation gradient tensor, as in the classical theory. This limiting PiolaKirchhoff stress tensor field is differentiable, and its divergence represents the force density due to internal forces. The limiting, or collapsed, stressstrain model satisfies the conditions in the classical theory for angular momentum balance, isotropy, objectivity, and hyperelasticity, provided the original peridynamic consti
Forces analysis for micromanipulation in dry and liquid media
 Journal of Micromechatronics
, 2006
"... During microscale object manipulation, contact (pulloff) forces and noncontact (capillary, van der Waals, and electrostatic) forces determine the behaviour of the microobjects rather than the inertial forces. The aim of this article is to give an experimental analysis of the physical phenomena a ..."
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Cited by 28 (19 self)
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During microscale object manipulation, contact (pulloff) forces and noncontact (capillary, van der Waals, and electrostatic) forces determine the behaviour of the microobjects rather than the inertial forces. The aim of this article is to give an experimental analysis of the physical phenomena at a microscopic scale in dry and liquid media. This article introduces a review of the major differences between dry and submerged micromanipulations. The theoretical influences of the medium on van der Waals forces, electrostatic forces, pulloff forces and hydrodynamic forces are presented. Experimental force measurements based on an AFM system are carried out. These experiments exhibit a correlation better than 40 % between the theoretical forces and the measured forces (except for pulloff in water). Finally, some comparative experimental micromanipulation results are described and show the advantages of the liquid medium
The Lubrication Approximation For Thin Viscous Films: The Moving Contact Line With A `porous Media' Cut Off Of Van Der Waals Interactions
 Nonlinearity
, 1994
"... . We consider the effect of a second order `porous media' [25] term on the evolution of weak solutions of the fourth order degenerate diffusion equation (1) h t = \Gammar \Delta (h n r\Deltah \Gamma rh m ) in one space dimension. The equation without the second order term is derived from a ..."
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Cited by 26 (8 self)
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. We consider the effect of a second order `porous media' [25] term on the evolution of weak solutions of the fourth order degenerate diffusion equation (1) h t = \Gammar \Delta (h n r\Deltah \Gamma rh m ) in one space dimension. The equation without the second order term is derived from a `lubrication approximation' and models surface tension dominated motion of thin viscous films and spreading droplets [18]. Here h(x; t) is the thickness of the film, and the physical problem corresponds to n = 3. For simplicity we consider periodic boundary conditions which has the physical interpretation of modeling a periodic array of droplets. In a previous work [6] we studied the above equation without the second order `porous media' term. In particular we showed the existence of nonnegative weak solutions with increasing support for 0 ! n ! 3 but the techniques failed for n 3. This is consistent with the fact that, in this case, nonnegative selfsimilar sourcetype solutions do not exist fo...
Dewetting Films: Bifurcations and concentrations
 NONLINEARITY
, 2001
"... Under the influence of longrange attractive and shortrange repulsive forces, thin liquid films rupture and form complex dewetting patterns. This paper studies this phenomenon in one space dimension within the framework of fourthorder degenerate parabolic equations of lubrication type. We derive t ..."
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Cited by 24 (10 self)
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Under the influence of longrange attractive and shortrange repulsive forces, thin liquid films rupture and form complex dewetting patterns. This paper studies this phenomenon in one space dimension within the framework of fourthorder degenerate parabolic equations of lubrication type. We derive the global structure of the bifurcation diagram for steadystate solutions. A stability analysis of the solution branches and numerical simulations suggest coarsening occurs. Furthermore, we study the behaviour of solutions in the limit that shortrange repulsive forces are neglected. Both asymptotic analysis and numerical experiments show that this limit can concentrate mass in δdistributions.
Dejan: Coarsening Rates for a Droplet Model: Rigorous Upper Bounds
"... Abstract. Certain liquids on solid substrates form a conguration of droplets connected by a precursor layer. This conguration coarsens: The average droplet size grows while the number of droplets decreases and the characteristic distance between them increases. We study this type of coarsening be ..."
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Cited by 24 (5 self)
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Abstract. Certain liquids on solid substrates form a conguration of droplets connected by a precursor layer. This conguration coarsens: The average droplet size grows while the number of droplets decreases and the characteristic distance between them increases. We study this type of coarsening behavior in a model given by an evolution equation for the lm height on an ndimensional substrate. Heuristic arguments based on the asymptotic analysis of Glasner and Witelski [6, 7] and numerical simulations suggest a statistically selfsimilar behavior characterized by a single exponent which determines the coarsening rate. In this paper, we establish rigorously an upper bound on the coarsening rate in a timeaveraged sense. We use the fact that the evolution is a gradient ow, i.e. a steepest descent in an energy landscape. Coarse information on the geometry of the energy landscape serves to obtain coarse information on the dynamics. This robust method was proposed in [10]. Our main analytical contribution is an interpolation inequality involving the Wasserstein distance which characterizes the coarse shape of the energy landscape. The upper bound we obtain is in agreement with heuristic arguments and numerical simulations. 1.
Linear Stability of Steady States for Thin Film and CahnHilliard Type Equations
, 2000
"... . We study the linear stability of smooth steady states of the evolution equation h t = (f(h)h xxx ) x (g(h)h x ) x ah under both periodic and Neumann boundary conditions. If a 6= 0 we assume f 1. In particular we consider positive periodic steady states of thin lm equations, where a = 0 and f; ..."
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Cited by 23 (4 self)
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. We study the linear stability of smooth steady states of the evolution equation h t = (f(h)h xxx ) x (g(h)h x ) x ah under both periodic and Neumann boundary conditions. If a 6= 0 we assume f 1. In particular we consider positive periodic steady states of thin lm equations, where a = 0 and f; g might have degeneracies such as f(0) = 0 as well as singularities like g(0) = +1. If a 0, we prove each periodic steady state is linearly unstable with respect to volume (area) preserving perturbations whose period is an integer multiple of the steady state's period. For area preserving perturbations having the same period as the steady state, we prove linear instability for all a if the ratio g=f is a convex function. Analogous results hold for Neumann boundary conditions. The rest of the paper concerns the special case of a = 0 and power law coecients f(y) = y n and g(y) = By m . We characterize the linear stability of each positive periodic steady state under perturbations of t...
Recognition of nucleic acid bases and basepairs by hydrogen bonding to amino acid sidechains
 J. Mol. Biol
, 2003
"... Sequencespecific protein–nucleic acid recognition is determined, in part, by hydrogen bonding interactions between amino acid sidechains and nucleotide bases. To examine the repertoire of possible interactions, we have calculated geometrically plausible arrangements in which amino acids hydrogen b ..."
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Cited by 22 (2 self)
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Sequencespecific protein–nucleic acid recognition is determined, in part, by hydrogen bonding interactions between amino acid sidechains and nucleotide bases. To examine the repertoire of possible interactions, we have calculated geometrically plausible arrangements in which amino acids hydrogen bond to unpaired bases, such as those found in RNA bulges and loops, or to the 53 possible RNA basepairs. We find 32 possible interactions that involve two or more hydrogen bonds to the six unpaired bases (including protonated A and C), 17 of which have been observed. We find 186 “spanning ” interactions to basepairs in which the amino acid hydrogen bonds to both bases, in principle allowing particular basepairs to be selectively targeted, and nine of these have been observed. Four calculated interactions span the Watson–Crick pairs and 15 span the G:U wobble pair, including two interesting arrangements with three hydrogen bonds to the Arg guanidinum group that have not yet been observed. The inherent donor–acceptor arrangements of the bases support many possible interactions to Asn (or Gln) and Ser (or Thr or Tyr), few interactions to Asp (or Glu) even though several already have been observed, and interactions to U (or T) only if the base is in an unpaired context, as also observed in several cases. This study highlights how complementary arrangements of donors and acceptors can contribute to basespecific recognition of RNA, predicts interactions not yet observed, and provides tools to analyze proposed contacts or design novel interactions.