184 research outputs found
Time-resolved measurement of the local equivalence ratio in a gaseous propane injection process using laser-induced gratings
This paper was published in Optics Express and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: http://www.opticsinfobase.org/abstract.cfm?URI=oe-14-26-12994. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law.Peer reviewedPublisher PD
Lateral phase separation of confined membranes
We consider membranes interacting via short, intermediate and long stickers.
The effects of the intermediate stickers on the lateral phase separation of the
membranes are studied via mean-field approximation. The critical potential
depth of the stickers increases in the presence of the intermediate sticker.
The lateral phase separation of the membrane thus suppressed by the
intermediate stickers. Considering membranes interacting with short and long
stickers, the effect of confinement on the phase behavior of the membranes is
also investigated analytically
Effective free energy for pinned membranes
We consider membranes adhered through specific receptor-ligand bonds. Thermal
undulations of the membrane induce effective interactions between adhesion
sites. We derive an upper bound to the free energy that is independent of
interaction details. To lowest order in a systematic expansion we obtain
two-body interactions which allow to map the free energy onto a lattice gas
with constant density. The induced interactions alone are not strong enough to
lead to a condensation of individual adhesion sites. A measure of the thermal
roughness is shown to depend on the inverse square root of the density of
adhesion sites, which is in good agreement with previous computer simulations.Comment: to appear as a Rapid Communication in Phys. Rev.
Random pinning limits the size of membrane adhesion domains
Theoretical models describing specific adhesion of membranes predict (for
certain parameters) a macroscopic phase separation of bonds into adhesion
domains. We show that this behavior is fundamentally altered if the membrane is
pinned randomly due to, e.g., proteins that anchor the membrane to the
cytoskeleton. Perturbations which locally restrict membrane height fluctuations
induce quenched disorder of the random-field type. This rigorously prevents the
formation of macroscopic adhesion domains following the Imry-Ma argument [Y.
Imry and S. K. Ma, Phys. Rev. Lett. 35, 1399 (1975)]. Our prediction of
random-field disorder follows from analytical calculations, and is strikingly
confirmed in large-scale Monte Carlo simulations. These simulations are based
on an efficient composite Monte Carlo move, whereby membrane height and bond
degrees of freedom are updated simultaneously in a single move. The application
of this move should prove rewarding for other systems also.Comment: revised and extended versio
An Effective Membrane Model of the Immunological Synapse
The immunological synapse is a patterned collection of different types of
receptors and ligands that forms in the intercellular junction between T Cells
and antigen presenting cells (APCs) during recognition. The synapse is
implicated in information transfer between cells, and is characterized by
different spatial patterns of receptors at different stages in the life cycle
of T cells. We obtain a minimalist model that captures this experimentally
observed phenomenology. A functional RG analysis provides further insights.Comment: 6 pages, 3 figures, submitted for publicatio
Phi-values in protein folding kinetics have energetic and structural components
Phi-values are experimental measures of how the kinetics of protein folding
is changed by single-site mutations. Phi-values measure energetic quantities,
but are often interpreted in terms of the structures of the transition state
ensemble. Here we describe a simple analytical model of the folding kinetics in
terms of the formation of protein substructures. The model shows that
Phi-values have both structural and energetic components. In addition, it
provides a natural and general interpretation of "nonclassical" Phi-values
(i.e., less than zero, or greater than one). The model reproduces the
Phi-values for 20 single-residue mutations in the alpha-helix of the protein
CI2, including several nonclassical Phi-values, in good agreement with
experiments.Comment: 15 pages, 3 figures, 1 tabl
Stable patterns of membrane domains at corrugated substrates
Multi-component membranes such as ternary mixtures of lipids and cholesterol
can exhibit coexistence regions between two liquid phases. When such membranes
adhere to a corrugated substrate, the phase separation process strongly depends
on the interplay between substrate topography, bending rigidities, and line
tension of the membrane domains as we show theoretically via energy
minimization and Monte Carlo simulations. For sufficiently large bending
rigidity contrast between the two membrane phases, the corrugated substrate
truncates the phase separation process and leads to a stable pattern of
membrane domains. Our theory is consistent with recent experimental
observations and provides a possible control mechanism for domain patterns in
biological membranes.Comment: to appear in Physical Review Letter
Dynamic phase separation of fluid membranes with rigid inclusions
Membrane shape fluctuations induce attractive interactions between rigid
inclusions. Previous analytical studies showed that the fluctuation-induced
pair interactions are rather small compared to thermal energies, but also that
multi-body interactions cannot be neglected. In this article, it is shown
numerically that shape fluctuations indeed lead to the dynamic separation of
the membrane into phases with different inclusion concentrations. The tendency
of lateral phase separation strongly increases with the inclusion size. Large
inclusions aggregate at very small inclusion concentrations and for relatively
small values of the inclusions' elastic modulus.Comment: 6 pages, 6 figure
Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations
Understanding and control of structures and rates involved in protein-ligand binding are es- sential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations cannot di- rectly sample the excessively long residence and rearrangement times of tightly binding complexes. Here we exploit the recently developed multi-ensemble Markov model framework to compute full protein-peptide kinetics of the oncoprotein fragment 25−109Mdm2 and the nano-molar inhibitor peptide PMI. Using this system, we report, for the first time, direct estimates of kinetics beyond the seconds timescales using simulations of an all-atom MD model, with high accuracy and pre- cision. These results only require explicit simulations on the sub-milliseconds timescale and are tested against existing mutagenesis data and our own experimental measurements of the dissoci- ation and association rates. The full kinetic model reveals an overall downhill but rugged binding funnel with multiple pathways. The overall strong binding arises from a variety of conformations with different hydrophobic contact surfaces that interconvert on the milliseconds timescale.Funding is acknowledged by European Commission (ERC StG “pcCells” to F.N.), Deutsche Forschungsgemeinschaft (SFB 1114/C3, SFB 740/D7, and TRR 186/A12 to F.N. and SFB 1114/A4 to F.N. and T.W.). J.C. is a Wellcome Trust Senior Research Fellow (WT 095195MA). J.S. is a Marie Sklodowska-Curie Internationally outgoing fellow. M.D.C. is supported by a Biotechnology and Biological Sciences Research Council (BBSRC) studentship
Effective surface interactions mediated by adhesive particles
In biomimetic and biological systems, interactions between surfaces are often
mediated by adhesive molecules, nanoparticles, or colloids dispersed in the
surrounding solution. We present here a general, statistical-mechanical model
for two surfaces that interact via adhesive particles. The effective,
particle-mediated interaction potential of the surfaces is obtained by
integrating over the particles' degrees of freedom in the partition function.
Interestingly, the effective adhesion energy of the surfaces exhibits a maximum
at intermediate particle concentrations, and is considerably smaller both at
low and high concentrations. The effective adhesion energy corresponds to a
minimum in the interaction potential at surface separations slightly larger
than the particle diameter, while a secondary minimum at surface contact
reflects depletion interactions. Our results can be generalized to surfaces
with specific receptors for solute particles, and have direct implications for
the adhesion of biomembranes and for phase transitions in colloidal systems.Comment: 6 pages, 5 figures; to appear in Europhys. Let
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