arXiv subjects

Todd Martinez

Publications and source records attributed to Todd Martinez.

7 recordsLinked to original sources

arXiv2026

Polyformer: a generative framework for thermodynamic modeling of polymeric molecules

The classic paradigm of structural biology is that the sequence of a biomolecule (protein, nucleic acid, lipid, etc) determines its conformation (shape) which determines its biological function. Protein folding programs like AlphaFold address this paradigm by predicting the single best conformation given a sequence that defines the molecule. However, biomolecules are not static structures, and their conformational ensemble determines their function. We present the Polyformer -- a generative framework for thermodynamic modeling of polymeric molecules. Given the sequence and temperature (or another thermodynamic variable), the Polyformer generates conformations faithful to the molecule's thermodynamic conformational ensemble. It is the first generative model that solves three problems simultaneously: how does a molecule fold, what is its conformational ensemble, and how does the conformational ensemble change as we change physical temperature. As a concrete test case, we apply Polyformer to protein domains with 50-111 residues and report good agreement of model predictions to Molecular Dynamics (MD) trajectories.

q-bio.BM↗

arXiv2020

Strictly Non-Adiabatic Quantum Control of the Acetylene Dication Using an Infrared Field

We demonstrate the existence of a strictly non-adiabatic control pathway in deprotonation of the acetylene dication. This pathway is identified experimentally by measuring a kinetic energy shift in an ion coincidence experiment. We use a TDSE simulation to identify which properties most strongly affect our control. We find that resonant control around conical intersections is limited by the speed of non-adiabatic dynamics.

physics.chem-ph↗

arXiv2018

Mixed Quantum-Classical Electrodynamics: Understanding Spontaneous Decay and Zero Point Energy

The dynamics of an electronic two-level system coupled to an electromagnetic field are simulated explicitly for one and three dimensional systems through semiclassical propagation of the Maxwell-Liouville equations. We consider three flavors of mixed quantum-classical dynamics: the classical path approximation (CPA), Ehrenfest dynamics, and symmetrical quantum-classical (SQC) dynamics. The CPA fails to recover a consistent description of spontaneous emission. A consistent "spontaneous" emission can be obtained from Ehrenfest dynamics--provided that one starts in an electronic superposition state. Spontaneous emission is always obtained using SQC dynamics. Using the SQC and Ehrenfest frameworks, we further calculate the dynamics following an incoming pulse, but here we find very different responses: SQC and Ehrenfest dynamics deviate sometimes strongly in the calculated rate of decay of the transient excited state. Nevertheless, our work confirms the earlier observations by W. Miller [J. Chem. Phys. 69, 2188-2195, 1978] that Ehrenfest dynamics can effectively describe some aspects of spontaneous emission and highlights new possibilities for studying light-matter interactions with semiclassical mechanics.

physics.optics↗

arXiv2017

Ultrafast Isomerization in Acetylene Dication: To Be or Not To Be

Experimental evidence has pointed toward the existence of ultrafast proton migration and isomerization as a key process for acetylene and its ions, however the actual mechanism for ultrafast isomerization of the acetylene [HCCH]2+ to vinylidene [H2CC]2+ dication remains nebulous. Theoretical studies show a high potential barrier of over 2eV for the isomerization pathways on the low lying dicationic states, implying that the corresponding isomerization should take picoseconds or even longer according to transition state theory. However a recent experiment at a femtosecond X-ray free electron laser (XFEL) [Nature Commun. 6, 8199 (2015)] suggests that large amplitude hydrogen migration proceeds on a sub-100 femtosecond time scale. In order to resolve the contradiction, we present a complete theoretical study of the dynamics of acetylene dication produced by Auger decay after X-ray photoionization of the carbon atom K shell. We find that isomerization does not occur on the sub-100 fs timescale and is not required to explain the time-resolved Coulomb imaging experiment. This study resolves the seeming contradiction between experiment and theory concerning the isomerization time scale in acetylene dication. This work calls for careful interpretation of structural information from the widely applied Coulomb momentum imaging method but also points out its strengths in mapping out momentum dispersion dynamics even when structural variation is minor.

physics.chem-ph↗

arXiv2013

Enhancement of strong-field multiple ionization in the vicinity of the conical intersection in 1,3-cyclohexadiene ring opening

Nonradiative energy dissipation in electronically excited polyatomic molecules proceeds through conical intersections, loci of degeneracy between electronic states. We observe a marked enhancement of laser-induced double ionization in the vicinity of a conical intersection during a non-radiative transition. We measured double ionization by detecting the kinetic energy of ions released by laser-induced strong-field fragmentation during the ring-opening transition between 1,3-cyclohexadiene and 1,3,5-hexatriene. The enhancement of the double ionization correlates with the conical intersection between the HOMO and LUMO orbitals.

physics.chem-ph↗

arXiv2013

Multiple orbital contributions to molecular high-harmonic generation in an asymmetric top

High-order harmonic generation (HHG) in aligned linear molecules can offer valuable information about strong-field interactions in lower-lying molecular orbitals, but extracting this information is difficult for three-dimensional molecular geometries. Our measurements of the asymmetric top SO2 show large axis dependencies, which change with harmonic order. The analysis shows that these spectral features must be due to field ionization and recombination from multiple orbitals during HHG. We expect that HHG can probe orbital dependencies using this approach for a broad class of asymmetric-top molecules.

physics.atom-ph↗

arXiv2013

Orientational decomposition of molecular high harmonic emission in three dimensions

An important goal in molecular physics and chemistry today is to obtain structure-dependent information about molecular function to obtain a deeper understanding into chemical reactions. However, until now, asymmetric tops, which comprise the widest and most general class of molecules, remain principally unexplored. This gap is particularly evident in high harmonic generation (HHG). HHG has successfully obtained structural information about electron hole pairs or orbitals for simple linear molecules. Unfortunately, for more complicated molecules, the emission from different molecular directions interfere, concealing individual angular signatures. Here we introduce a method to extract orientation-dependent information from asymmetric tops and apply it to the sulfur dioxide (SO2) molecule. We use the rotational revival structure to decompose the angular contributions of HHG emission. This method also extends HHG-based tomographic imaging into three dimensions and makes it applicable to a much wider class of systems than previously envisioned. Our results suggest that HHG is a powerful tool to probe electron orbital structure and dynamics of complex molecules.

physics.atom-ph↗