Aggregation of amphiphiles through the action of hydrophobic interactions is a common feature in soft condensed matter systems and is of particular importance in the context of biophysics as it underlies both the generation of functional biological m
achinery as well as the formation of pathological misassembled states of proteins. Here we explore the aggregation behaviour of amphiphilic polymers using lattice Monte-Carlo calculations and show that the distribution of hydrophobic residues within the polymer sequence determines the facility with which dry/wet interfaces can be created and that such interfaces drive the aggregation process.
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic contribution
s of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.
Colloids coated with single-stranded DNA (ssDNA) can bind selectively to other colloids coated with complementary ssDNA. The fact that DNA-coated colloids (DNACCs) can bind to specific partners opens the prospect of making colloidal `molecules. Howev
er, in order to design DNACC-based molecules, we must be able to control the valency of the colloids, i.e. the number of partners to which a given DNACC can bind. One obvious, but not very simple approach is to decorate the colloidal surface with patches of single-stranded DNA that selectively bind those on other colloids. Here we propose a design principle that exploits many-body effects to control the valency of otherwise isotropic colloids. Using a combination of theory and simulation, we show that we can tune the valency of colloids coated with mobile ssDNA, simply by tuning the non-specific repulsion between the particles. Our simulations show that the resulting effective interactions lead to low-valency colloids self-assembling in peculiar open structures, very different from those observed in DNACCs with immobile DNA linkers.
Recently 1, we presented a general theory for calculat- ing the strength and properties of colloidal interactions mediated by ligand-receptor bonds (such as those that bind DNA-coated colloids). In this communication, we derive a surprisingly simple
analytical form for the inter- action free energy, which was previously obtainable only via a costly numerical thermodynamic integration. As a result, the computational effort to obtain potentials of in- teraction is significantly reduced. Moreover, we can gain insight from this analytic expression for the free energy in limiting cases. In particular, the connection of our general theory to other previous specialised approaches is now made transparent. This important simplification will significantly broaden the scope of our theory.
We use transition path sampling to study evaporation in the SPC/E model of liquid water. Based on thousands of evaporation trajectories, we characterize the members of the transition state ensemble (TSE), which exhibit a liquid-vapor interface with p
redominantly negative mean curvature at the site of evaporation. We also find that after evaporation is complete, the distributions of translational and angular momenta of the evaporated water are Maxwellian with a temperature equal to that of the liquid. To characterize the evaporation trajectories in their entirety, we find that it suffices to project them onto just two coordinates: the distance of the evaporating molecule to the instantaneous liquid-vapor interface, and the velocity of the water along the average interface normal. In this projected space, we find that the TSE is well-captured by a simple model of ballistic escape from a deep potential well, with no additional barrier to evaporation beyond the cohesive strength of the liquid. Equivalently, they are consistent with a near-unity probability for a water molecule impinging upon a liquid droplet to condense. These results agree with previous simulations and with some, but not all, recent experiments.
We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the configurational and co
mbinatorial entropic factors that play a key role in valence-limited interactions. By rigorously enforcing self-consistency, it achieves near-quantitative accuracy with respect to detailed Monte Carlo calculations. With suitable approximations and in particular geometries, our theory reduces to previous successful treatments, which are now united in a common and extensible framework. We expect our tools to be useful to other researchers investigating ligand-mediated interactions. A complete and well-documented Python implementation is freely available at http://github.com/patvarilly/DNACC .
Water near hydrophobic surfaces is like that at a liquid-vapor interface, where fluctuations in water density are substantially enhanced compared to that in bulk water. Here we use molecular simulations with specialized sampling techniques to show th
at water density fluctuations are similarly enhanced, even near hydrophobic surfaces of complex biomolecules, situating them at the edge of a dewetting transition. Consequently, water near these surfaces is sensitive to subtle changes in surface conformation, topology, and chemistry, any of which can tip the balance towards or away from the wet state, and thus significantly alter biomolecular interactions and function. Our work also resolves the long-standing puzzle of why some biological surfaces dewet and other seemingly similar surfaces do not.
Interfaces are a most common motif in complex systems. To understand how the presence of interfaces affect hydrophobic phenomena, we use molecular simulations and theory to study hydration of solutes at interfaces. The solutes range in size from sub-
nanometer to a few nanometers. The interfaces are self-assembled monolayers with a range of chemistries, from hydrophilic to hydrophobic. We show that the driving force for assembly in the vicinity of a hydrophobic surface is weaker than that in bulk water, and decreases with increasing temperature, in contrast to that in the bulk. We explain these distinct features in terms of an interplay between interfacial fluctuations and excluded volume effects---the physics encoded in Lum-Chandler-Weeks theory [J. Phys. Chem. B 103, 4570--4577 (1999)]. Our results suggest a catalytic role for hydrophobic interfaces in the unfolding of proteins, for example, in the interior of chaperonins and in amyloid formation.
Water density fluctuations are an important statistical mechanical observable that is related to many-body correlations, as well as hydrophobic hydration and interactions. Local water density fluctuations at a solid-water surface have also been propo
sed as a measure of its hydrophobicity. These fluctuations can be quantified by calculating the probability, $P_v(N)$, of observing $N$ waters in a probe volume of interest $v$. When $v$ is large, calculating $P_v(N)$ using molecular dynamics simulations is challenging, as the probability of observing very few waters is exponentially small, and the standard procedure for overcoming this problem (umbrella sampling in $N$) leads to undesirable impulsive forces. Patel et al. [J. Phys. Chem. B, 114, 1632 (2010)] have recently developed an indirect umbrella sampling (INDUS) method, that samples a coarse-grained particle number to obtain $P_v(N)$ in cuboidal volumes. Here, we present and demonstrate an extension of that approach to other basic shapes, like spheres and cylinders, as well as to collections of such volumes. We further describe the implementation of INDUS in the NPT ensemble and calculate $P_v(N)$ distributions over a broad range of pressures. Our method may be of particular interest in characterizing the hydrophobicity of interfaces of proteins, nanotubes and related systems.
