2,385 research outputs found
Systematic characterization of thermodynamic and dynamical phase behavior in systems with short-ranged attraction
In this paper we demonstrate the feasibility and utility of an augmented
version of the Gibbs ensemble Monte Carlo method for computing the phase
behavior of systems with strong, extremely short-ranged attractions. For
generic potential shapes, this approach allows for the investigation of
narrower attractive widths than those previously reported. Direct comparison to
previous self-consistent Ornstein-Zernike approximation calculations are made.
A preliminary investigation of out-of-equilibrium behavior is also performed.
Our results suggest that the recent observations of stable cluster phases in
systems without long-ranged repulsions are intimately related to gas-crystal
and metastable gas-liquid phase separation.Comment: 10 pages, 8 figure
Crystallization and gelation in colloidal systems with short-ranged attractive interactions
We systematically study the relationship between equilibrium and
non-equilibrium phase diagrams of a system of short-ranged attractive colloids.
Using Monte Carlo and Brownian dynamics simulations we find a window of
enhanced crystallization that is limited at high interaction strength by a
slowing down of the dynamics and at low interaction strength by the high
nucleation barrier. We find that the crystallization is enhanced by the
metastable gas-liquid binodal by means of a two-stage crystallization process.
First, the formation of a dense liquid is observed and second the crystal
nucleates within the dense fluid. In addition, we find at low colloid packing
fractions a fluid of clusters, and at higher colloid packing fractions a
percolating network due to an arrested gas-liquid phase separation that we
identify with gelation. We find that this arrest is due to crystallization at
low interaction energy and it is caused by a slowing down of the dynamics at
high interaction strength. Likewise, we observe that the clusters which are
formed at low colloid packing fractions are crystalline at low interaction
energy, but glassy at high interaction energy. The clusters coalesce upon
encounter.Comment: 8 pages, 8 figure
Reverse-selective diffusion in nanocomposite membranes
The permeability of certain polymer membranes with impenetrable
nanoinclusions increases with the particle volume fraction (Merkel et al.,
Science, 296, 2002). This intriguing observation contradicts even qualitative
expectations based on Maxwell's classical theory of conduction/diffusion in
composites with homogeneous phases. This letter presents a simple theoretical
interpretation based on classical models of diffusion and polymer physics. An
essential feature of the theory is a polymer-segment depletion layer at the
inclusion-polymer interface. The accompanying increase in free volume leads to
a significant increase in the local penetrant diffusivity, which, in turn,
increases the bulk permeability while exhibiting reverse selectivity. This
model captures the observed dependence of the bulk permeability on the
inclusion size and volume fraction, providing a straightforward connection
between membrane microstructure and performance
Quantitation of intracellular NAD(P)H can monitor an imbalance of DNA single strand break repair in base excision repair deficient cells in real time
DNA single strand breaks (SSBs) are one of the most frequent DNA lesions in genomic DNA generated either by oxidative stress or during the base excision repair pathways. Here we established a new real-time assay to assess an imbalance of DNA SSB repair by indirectly measuring PARP-1 activation through the depletion of intracellular NAD(P)H. A water-soluble tetrazolium salt is used to monitor the amount of NAD(P)H in living cells through its reduction to a yellow colored water-soluble formazan dye. While this assay is not a direct method, it does not require DNA extraction or alkaline treatment, both of which could potentially cause an artifactual induction of SSBs. In addition, it takes only 4 h and requires less than a half million cells to perform this measurement. Using this assay, we demonstrated that the dose- and time-dependent depletion of NAD(P)H in XRCC1-deficient CHO cells exposed to methyl methanesulfonate. This decrease was almost completely blocked by a PARP inhibitor. Furthermore, methyl methanesulfonate reduced NAD(P)H in PARP-1+/+cells, whereas PARP-1¿/¿ cells were more resistant to the decrease in NAD(P)H. These results indicate that the analysis of intracellular NAD(P)H level using water-soluble tetrazolium salt can assess an imbalance of SSB repair in living cells in real time
Genetic structure of Ilyoplax delsmani (Crustacea: Decapoda: Brachyura: Dotillidae) on the western Indonesian waters
The 5th International Conference on Biosciences 02/08/2023 - 03/08/2023 Bogor, IndonesiaEstuarine crab disperses passively to different areas during their larval stage through sea currents. Ilyoplax delsmani, one of the estuarine crabs, is widely distributed in the Indo-Malaysia Archipelago. The present study aims to discern the genetic structure of Ilyoplax delsmani in the western part of Indonesia. Specimens were collected from three sites, i.e. one site in Kalimantan and two sites in Java Island. We analyzed the genetic structure of I. delsmani with COI gene using MEGA-X, DNASP v6.12.03, Arlequin v3.5.2.2., and Network v10.2. The constructed phylogenetic tree with MEGA-X with maximum likelihood (ML) using Kimura 2 parameter based on the COI gene revealed two distinct clades, i.e., Kalimantan_5133-Java_5135 as Clade 1 and Java_5136 as Clade 2. The genetic distance within the clade range from 0.2% to 2.2%, meanwhile the distance between the clades is approximately 19.3%–20.7%. Moreover, the haplotype network and FST values calculated between pairs of localities generate a congruent result with the phylogenetic tree. Through calculation using MEGA-X, we estimate that the divergence time between both clades is approximately 42.49 mya, aligning with the middle Eocene period. Hence, we deduce that both clades represent distinct species
Structure and thermodynamics of colloid-polymer mixtures: a macromolecular approach
The change of the structure of concentrated colloidal suspensions upon
addition of non-adsorbing polymer is studied within a two-component,
Ornstein-Zernicke based liquid state approach. The polymers' conformational
degrees of freedom are considered and excluded volume is enforced at the
segment level. The polymer correlation hole, depletion layer, and excess
chemical potentials are described in agreement with polymer physics theory in
contrast to models treating the macromolecules as effective spheres. Known
depletion attraction effects are recovered for low particle density, while at
higher densities novel many-body effects emerge which become dominant for large
polymers.Comment: 7 pages, 4 figures; to be published in Europhys. Let
Entropic torque
Quantitative predictions are presented of a depletion-induced torque and
force acting on a single colloidal hard rod immersed in a solvent of hard
spheres close to a planar hard wall. This torque and force, which are entirely
of entropic origin, may play an important role for the key-lock principle,
where a biological macromolecule (the key) is only functional in a particular
orientation with respect to a cavity (the lock)
Helical Tubes in Crowded Environments
When placed in a crowded environment, a semi-flexible tube is forced to fold
so as to make a more compact shape. One compact shape that often arises in
nature is the tight helix, especially when the tube thickness is of comparable
size to the tube length. In this paper we use an excluded volume effect to
model the effects of crowding. This gives us a measure of compactness for
configurations of the tube, which we use to look at structures of the
semi-flexible tube that minimize the excluded volume. We focus most of our
attention on the helix and which helical geometries are most compact. We found
that helices of specific pitch to radius ratio 2.512 to be optimally compact.
This is the same geometry that minimizes the global curvature of the curve
defining the tube. We further investigate the effects of adding a bending
energy or multiple tubes to begin to explore the more complete space of
possible geometries a tube could form.Comment: 10 page
Monte Carlo simulations of the solid-liquid transition in hard spheres and colloid-polymer mixtures
Monte Carlo simulations at constant pressure are performed to study
coexistence and interfacial properties of the liquid-solid transition in hard
spheres and in colloid-polymer mixtures. The latter system is described as a
one-component Asakura-Oosawa (AO) model where the polymer's degrees of freedom
are incorporated via an attractive part in the effective potential for the
colloid-colloid interactions. For the considered AO model, the polymer
reservoir packing fraction is eta_p^r=0.1 and the colloid-polymer size ratio is
q=sigma_p/\sigma=0.15 (with sigma_p and sigma the diameter of polymers and
colloids, respectively). Inhomogeneous solid-liquid systems are prepared by
placing the solid fcc phase in the middle of a rectangular simulation box
creating two interfaces with the adjoined bulk liquid. By analyzing the growth
of the crystalline region at various pressures and for different system sizes,
the coexistence pressure p_co is obtained, yielding p_co=11.576 k_BT/sigma^3
for the hard sphere system and p_co=8.0 k_BT/sigma^3 for the AO model (with k_B
the Boltzmann constant and T the temperature). Several order parameters are
introduced to distinguish between solid and liquid phases and to describe the
interfacial properties. From the capillary-wave broadening of the solid-liquid
interface, the interfacial stiffness is obtained for the (100) crystalline
plane, giving the values gamma=0.49 k_BT/sigma^2 for the hard-sphere system and
gamma=0.95 k_BT/sigma^2 for the AO model.Comment: 11 pages, 13 figure
Description of the fluctuating colloid-polymer interface
To describe the full spectrum of surface fluctuations of the interface
between phase-separated colloid-polymer mixtures from low scattering vector q
(classical capillary wave theory) to high q (bulk-like fluctuations), one must
take account of the interface's bending rigidity. We find that the bending
rigidity is negative and that on approach to the critical point it vanishes
proportionally to the interfacial tension. Both features are in agreement with
Monte Carlo simulations.Comment: 5 pages, 3 figures, 1 table. Accepted for publication in Phys. Rev.
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