相关论文: Simple approach for calculating the binding free e…
Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although, complex functionalities often emerge from the simultaneous interaction of…
We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…
Multivalent particles competing for binding on the same surface can exhibit switch-like behaviour, depending on the concentration of receptors on the surface. When the receptor concentration is low, energy dominates the free energy of…
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…
We present relativistic many-body calculations of total electron binding energy of neutral atoms up to element $Z=120$. Binding energy for ions may be found by subtracting known ionization potentials. Accuracy of the results for $17<Z…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor…
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…
We compute the high-dimensional limit of the free energy associated with a multi-layer generalized linear model. Under certain technical assumptions, we identify the limit in terms of a variational formula. The approach is to first show…
We present a method which computes many-electron energies and eigenfunctions by a full configuration interaction which uses a basis of atomistic tight-binding wave functions. This approach captures electron correlation as well as atomistic…
We consider $N$ bosons in a box in $\mathbb {R}^d$ with volume $N/\rho$ under the influence of a mutually repellent pair potential. The particle density $\rho\in (0,\infty)$ is kept fixed. Our main result is the identification of the…
Multivalent particles have the ability to form multiple bonds to a substrate. Hence, a multivalent interaction can be strong, even if the individual bonds are weak. However, much more interestingly, multivalency greatly increases the…
Application of the principle of energy balance to a rigid indenter in contact with elastic layer on a flat rigid substrate provides a very simple derivation of the detachment criterion which earlier has been obtained by much more…
We present a simple one-dimensional quantum-mechanical model for a particle attached to a surface. We solve the Schr\"odinger equation in terms of Weber functions and discuss the behavior of the eigenvalues and eigenfunctions. We derive the…
A theoretical approach has been undertaken in order to model the thermodynamic equilibrium of a vesicle adhering to a flat substrate. The vesicle is treated in a canonical description with a fixed number of sites. A finite number of these…
Targeted drug delivery relies on two physical processes: the selective binding of a therapeutic particle to receptors on a specific cell membrane, followed by transport of the particle across the membrane. In this article, we address some…
We perform an ab-initio calculation for the binding energy of ${}^6Li$ using the CD-Bonn 2000 NN potential renormalized with the Lee-Suzuki method. The many-body approach to the problem is the Hybrid Multideterminant method. The results…
Multivalent particles bind to targets via many independent ligand-receptor bonding interactions. This microscopic design spans length scales in both synthetic and biological systems. Classic examples include interactions between cells,…
We present an extension of Alchemical Transfer Method (ATM) for the estimation of relative binding free energies of molecular complexes applicable to conventional as well as scaffold-hopping alchemical transformations. The method, named…
A variational approach is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic energy containing monomer-monomer force constants…