Guillermo Pérez-Hernández

Guillermo Pérez-Hernández
Freie Universität Berlin | FUB · Institute of Mathematics

Dr. rer. nat.

About

22
Publications
3,880
Reads
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2,011
Citations
Citations since 2017
5 Research Items
1729 Citations
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20172018201920202021202220230100200300
20172018201920202021202220230100200300
20172018201920202021202220230100200300
Introduction
Additional affiliations
February 2014 - August 2014
Memorial Sloan Kettering Cancer Center
Position
  • PostDoc Position
December 2010 - present
Freie Universität Berlin
Position
  • Researcher
Description
  • http://compmolbio.biocomputing-berlin.de/
October 2007 - December 2010
Friedrich Schiller University Jena
Position
  • Staff Scientist - PhD-Student

Publications

Publications (22)
Article
Full-text available
Abstract The rise of multi-drug resistance in bacterial pathogens is one of the grand challenges facing medical science. A major concern is the speed of development of β-lactamase-mediated resistance in Gram-negative species, thus putting at risk the efficacy of the most recently approved antibiotics and inhibitors, including carbapenems and avibac...
Article
Full-text available
We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 µs long, ~162 µs in total) complemented by Replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and...
Research
Full-text available
The Molecular Projection Explorer, molPX, is a python module that provides interactive visualization of projected coordinates of molecular dynamics (MD) trajectories inside a Jupyter notebook. molPX is based on the incredibly useful nglview IPython/Jupyter widget.
Article
Analysis of molecular dynamics, for example using Markov models, often require the identification of order parameters that are good indicators of the rare events, i.e. good reaction coordinates. Recently, it has been shown that the time-lagged independent component analysis (TICA) finds the linear combinations of input coordinates that optimally re...
Article
Full-text available
Markov (state) models (MSMs) and related models of molecular kinetics have recently received a surge of interest as they can systematically reconcile simulation data from either a few long or many short simulations and allow us to analyze the essential metastable structures, thermodynamics, and kinetics of the molecular system under investigation....
Article
The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here, we present a variational approach for computing these dominant ei...
Article
Full-text available
A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes via (i) identification of the structural changes involved in these processes and (ii) estimation of the rates or timescales at which these slow processes occur. Most of the approaches to this task, including Markov models, master-eq...
Article
Effective Lennard-Jones models for the water-carbon interaction are derived from existing high-level ab initio calculations of water adsorbed on graphene models. The resulting potential energy well (ε(CO) + 2ε(CH) ≈ 1 kJ mol(-1)) is deeper than most of the previously used values in the literature on water in carbon nanotubes (CNTs). Moreover, a sub...
Article
The electronic excited states corresponding to singlet oxygen generation versus O–O splitting in o-fluorine-phenyl-9-anthracene-9,10-endoperoxide 1 and its 9,10-bisarylanthracene analog 2 have been investigated using theoretical methods. In the case of the smaller endoperoxide 1, the recently developed second-order perturbation theory restricted ac...
Article
A four dimensional (4D) time-dependent calculation to obtain the first vibrational states of the hydrogen bifluoride ion, FHF(-), and its deuterated counterpart, FDF(-), has been performed using a spectral method in Cartesian coordinates. The corresponding potential energy surfaces have been computed at the CCSD(T)/aug-cc-pVTZ level of theory. The...
Article
The excited state dynamics of 2-cyclopentylidene-tetrahydrofuran (CPTHF) is investigated using quantum dynamics. CPTHF can be considered a model for an asymmetric molecular rotor in which unidirectional rotation could be triggered around the double bond. After excitation, conical intersections at twisted angles allow for rationless decay to the gro...
Article
Chiral overcrowded alkenes are capable of unidirectional rotation via a series of cis-trans photochemical and helix-inversion thermal steps. Using a pseudo-random conformational search we have located different ground state minima belonging to the potential energy surface of two different overcrowded alkenes that function as molecular rotors. The t...
Article
The ground state potential energy surface of the model molecular rotor 2-cyclopentylidene-tetrahydrofuran (CPTHF) has been characterized by calculating minimum energy conformations, racemization pathways, and rotational barriers with high level ab initio electronic structure calculations. Two conformers with their corresponding enantiomers are foun...
Article
Full-text available
We investigate the extent to which unidirectional intramolecular torsional motion can be created in an oriented bicyclic model system driven solely by laser light. We apply the machinery of quantum control via specifically tailored laser pulses to induce such motion, eliminating the need for the thermally constrained steps conventionally used in mo...
Article
The UV-vis absorption spectra of the photoreceptor chromophores biliverdin (BV) in the ZZZssa conformation and the phycocyanobilin (PCB) with conformations ZZZssa and ZZZasa have been investigated by means of time-dependent density functional theory (TD-DFT) with a polarized continuum model. The three systems are studied in different conditions to...
Article
The electronic excited states of the olefin 1,1'-bicylohexylidene (BCH) are investigated using multiconfigurational complete active space self-consistent-field second order perturbation theory in its multi-state version (MS-CASPT2). Our calculations undoubtedly show that the bulk of the intensity of the two unusually intense bands of the UV absorpt...
Article
We present hydrogen bonds with toroidal densities of the protons, called toroidal hydrogen bonds, in systems with cylindrical symmetry e.g. triatomic molecules AHB or ions AHB(+) or AHB(-). These may be prepared by excitation of the degenerate bending vibrations and related pseudorotation such that the hydrogen atom (or the corresponding proton) is...
Article
Control of time-dependent wavepackets in the frame of unimolecular reactions is described. The shown applications include photodissociation and photoisomerization dynamics in three isolated systems.

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