Leonor Saiz

Hydrogen bonding in liquid alcohols: a computer simulation study

Abstract A series of molecular dynamics simulations has been performed to investigate hydrogen bonding in liquid alcohols. The systems considered have been methanol, ethanol, ethylene glycol and glycerol at 298 K. The hydrogen bonding statistics as well as the mean lifetime of the hydrogen bonds are analyzed. The results are compared with those corresponding to liquid water.

Structural Properties of a Highly Polyunsaturated Lipid Bilayer from Molecular Dynamics Simulations

The structure of a fully hydrated mixed (saturated/polyunsaturated) chain lipid bilayer in the biologically relevant liquid crystalline phase has been examined by performing a molecular dynamics study. The model membrane, a 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC, 18:0/22:6 PC) lipid bilayer, was investigated at constant (room) temperature and (ambient) pressure, and the results obtained in the nanosecond time scale reproduced quite well the available experimental data. Polyunsaturated fatty acids are found in high concentrations in neuronal and retinal tissues and are essential for the development of human brain function. The docosahexaenoic fatty acid, in particular, is fundamental for the proper function of the visual receptor rhodopsin. The lipid bilayer order has been investigated through the orientational order parameters. The water-lipid interface has been explored thoroughly in terms of its dimensions and the organization of the different components. Several types of interactions occurring in the system have been analyzed, specifically, the water-hydrocarbon chain, lipid-lipid and lipid-water interactions. The distribution of dihedral angles along the chains and the molecular conformations of the polyunsaturated chain of the lipids have also been studied. Special attention has been focused on the microscopic (molecular) origin of the effects of polyunsaturations on the different physical properties of membranes.

DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise.

The formation of DNA loops by the binding of proteins and protein complexes at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination and replication. Important thermodynamic concepts underlie the assembly of macromolecular complexes on looped DNA. The effects that this process has on the properties of gene regulation extend beyond the traditional view of DNA looping as a mechanism to increase the affinity of regulatory molecules for their cognate sites. Recent developments indicate that DNA looping can also lead to the suppression of cell-to-cell variability, the control of transcriptional noise, and the activation of cooperative interactions on demand.

DNA looping : the consequences and its control

The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination and replication. Recently, advances have been made in understanding the properties of DNA looping in its natural context and how they propagate to cellular behavior through gene regulation. The result of connecting the molecular properties of DNA looping with cellular physiology measurements indicates that looping of DNA in vivo is much more complex and easier than predicted from current models, and reveals a wealth of previously unappreciated details.

Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations

The organization of the lipid headgroups in a neutral model membrane is studied by atomistic simulations in the fluid lamellar phase, Lα. In particular, we report the results obtained for a fully hydrated 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine lipid bilayer at room temperature. The orientational distribution of the lipid dipole moments with respect to the membrane normal presents a maximum at 70° (20° above the plane of the interface, pointing toward the water region). We also found another smaller peak at 110° (−20° with respect to the membrane plane). This preferential orientation of the lipid headgroup dipoles with respect to the bilayer normal obtained at 303 K is qualitatively different from previous calculations at higher temperatures in the fluid lamellar phase, where headgroup dipoles were uniformly distributed with orientations spanning 0°–135°. Despite their differences, both situations give rise to a similar mean orientation of ∼70°, which is in excellent agreement with experi...

Structure of liquid ethylene glycol: A molecular dynamics simulation study with different force fields

The structure of liquid ethylene glycol at room temperature is examined by performing molecular dynamics (MD) simulation studies for several different liquid phase force fields. We compare the properties obtained and analyze the differences which arise from the use of these models. A thorough study of molecular conformation and intermolecular structure for the different potential models is carried out given that three of the studied force fields have the same intermolecular parameters and different intramolecular interactions. In addition, the effect of molecular shape on the intermolecular structure is discussed. Due to the important role played by the highly directional forces occurring in hydrogen bonded systems, in their intermolecular structure and in the macroscopic properties of the system, we pay special attention to the analysis of the features of the hydrogen bonding patterns present in the liquid. Revealing an overall agreement with the available structural experimental data, the results obtained show that, for the simulated models, the intermolecular structure is rather similar. The dynamics of the system is studied through the self-diffusion coefficients and, in contrast to the structural properties, the results obtained for the distinct models are quite different.

Dynamics in hydrogen bonded liquids: water and alcohols

Molecular dynamics (MD) has been revealed as a powerful tool to investigate the structure and dynamics of hydrogen bonded liquids. This paper reviews recent works in which MD simulations have been used to study the influence of hydrogen bonding on different dynamic properties of liquid water and alcohols. The analysed properties include intermolecular vibrations, self-diffusion coefficients and reorientational correlation times. Finally, we present a MD study of the translational and reorientational dynamics of supercooled water at pressures up to 400 MPa. The influence of hydrogen bonding on the anomalous behaviour of the dynamic properties of liquid water at high pressures and low temperatures is discussed.

Towards an Understanding of Complex Biological Membranes from Atomistic Molecular Dynamics Simulations

Computer simulation has emerged as a powerful tool for studying the structural and functional properties of complex biological membranes. In the last few years, the use of recently developed simulation methodologies and current generation force fields has permitted novel applications of molecular dynamics simulations, which have enhanced our understanding of the different physical processes governing biomembrane structure and dynamics. This review focuses on frontier areas of research with important biomedical applications. We have paid special attention to polyunsaturated lipids, membrane proteins and ion channels, surfactant additives in membranes, and lipid–DNA gene transfer complexes.

Dielectric properties of liquid ethanol. A computer simulation study

Static and dynamic dielectric properties of liquidethanol have been studied as a function of the wave-vector number by computer simulation.Molecular dynamics simulations at room temperature have been performed using the optimized potentials for liquid simulations (OPLS) potential model proposed by Jorgensen [J. Phys. Chem. 90, 1276 (1986)]. The time dependent correlation functions of the longitudinal and transverse components of the dipole density as well as the individual and total dipole moment autocorrelation functions have been calculated. The infrared spectra and the dielectric relaxation of the liquid have been also analyzed. Results have been compared with the available experimental data. Special attention has been dedicated to investigate the molecular origin of the different analyzed properties.

Stochastic dynamics of macromolecular-assembly networks.

The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components give rise to systemic properties of cells. Here, we present a stochastic approach to study the dynamics of networks formed by macromolecular complexes in terms of the molecular interactions of their components. Exploiting key thermodynamic concepts, this approach makes it possible to both estimate reaction rates and incorporate the resulting assembly dynamics into the stochastic kinetics of cellular networks. As prototype systems, we consider the lac operon and phage λ induction switches, which rely on the formation of DNA loops by proteins and on the integration of these protein–DNA complexes into intracellular networks. This cross‐scale approach offers an effective starting point to move forward from network diagrams, such as those of protein–protein and DNA–protein interaction networks, to the actual dynamics of cellular processes.