Andres Jaramillo-Botero

• Ph.D.
• Director at California Institute of Technology

We designed, developed, and clinically tested two rapid antigen-based immunosensors for SARS-CoV-2 detection, enabling diagnosis and viral load quantification for under USD $2. In a first clinical study, a screen-printed disposable carbon-based (SPC) sensor was assessed on prospectively recruited adult participants classified into three study group...

Cervical cancer is predominantly caused by human papillomavirus (HPV), with oncogenic strains HPV 16 and 18 accounting for most cases worldwide. Prompt and precise identification of these high-risk HPV types is essential for enhancing patient outcomes as it enables timely intervention and management. However, the existing HPV detection techniques a...

Aluminum in its Al³⁺ form is a metal that inhibits plant growth, especially in acidic soils (pH < 5.5). Rapid and accurate quantitative detection of Al³⁺ in agricultural soils is critical for the timely implementation of remediation strategies. However, detecting metal ions requires time-consuming preparation of samples, using expensive instrumenta...

Aluminum in its Al ³⁺ form is a metal that inhibits plant growth, especially in acidic soils (pH < 5.5). Rapid and accurate quantitative detection of Al ³⁺ in agricultural soils is critical for the timely implementation of remediation strategies. However, detecting metal ions requires time-consuming preparation of samples, using expensive instrumen...

Background The intersection of artificial intelligence (AI) with cancer research is increasing, and many of the advances have focused on the analysis of cancer images. Objectives To describe and synthesize the literature on the diagnostic accuracy of AI in early imaging diagnosis of cervical cancer following Preferred Reporting Items for Systemati...

The use of Unmanned Aerial Vehicle (UAV) images for biomass and nitrogen estimation offers multiple opportunities for improving rice yields. UAV images provide detailed, high-resolution visual information about vegetation properties, enabling the identification of phenotypic characteristics for selecting the best varieties, improving yield predicti...

Plant stress responses involve a suite of genetically encoded mechanisms triggered by real-time interactions with their surrounding environment. Although sophisticated regulatory networks maintain proper homeostasis to prevent damage, the tolerance thresholds to these stresses vary significantly among organisms. Current plant phenotyping techniques...

GCR1 has been proposed as a plant analogue to animal G-protein-coupled receptors that can promote or regulate several physiological processes by binding different phytohormones. For instance, abscisic acid (ABA) and gibberellin A1 (GA1) have been shown to promote or regulate germination and flowering, root elongation, dormancy, and biotic and abiot...

[This corrects the article DOI: 10.3389/fpls.2022.992663.].

Laser-induced graphene (LIG) uses a CO2 infrared laser scriber for transforming specific polymer substrates into porous graphene. This technique is simple, scalable, low-cost, free of chemicals, and produces a 3D graphene for applications across many fields. However, the resulting 3D graphene is highly sensitive to the lasing parameters used in the...

Sucrose is a primary metabolite in plants, a source of energy, a source of carbon atoms for growth and development, and a regulator of biochemical processes. Most of the traditional analytical chemistry methods for sucrose quantification in plants require sample treatment (with consequent tissue destruction) and complex facilities, that do not allo...

In the present work, PVDF - Fe3O4 nanoparticle (NP) nanocomposite films were produced using the electrospinning method. We investigated the effect of NP size on the film's morphology (fiber size), mechanical properties, and physical properties (β-phase percentage). Surprisingly, while nanoparticle size acts as an enhancer for mechanical properties,...

The OMICAS alliance is part of the Colombian government’s Scientific Ecosystem, established between 2017-2018 to promote world-class research, technological advancement and improved competency of higher education across the nation. Since the program’s kick-off, OMICAS has focused on consolidating and validating a multi-scale, multi-institutional, m...

The quantification of heavy metals is crucial to many different applications, and particularly relevant to agriculture. Here we describe an electrochemical sensor to detect and quantify ultra-low concentrations of aluminum in solutions. High aluminum levels are associated with inadequate crop development, growth, and production. To this end, we dem...

The 21st century has already brought us a plethora of new threats related to viruses that emerge in humans after zoonotic transmission or drastically change their geographic distribution or prevalence. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first spotted at the end of 2019 to rapidly spread in southwest Asia and later caus...

Nanosensors to detect and measure biomarkers are increasingly pervasive in our daily lives. Nanostructured materials provide an unprecedented opportunity to measure ultra-low concentrations (<nM L⁻¹) of target analytes, which in turn enables improved understanding of complex biological processes. Sensors with low detection limits serve multiple rol...

A critical path to solving the SARS-CoV-2 pandemic, without further socioeconomic impact, is to stop its spread. For this to happen, pre- or asymptomatic individuals infected with the virus need to be detected and isolated opportunely. Unfortunately, there are no current ubiquitous (i.e., ultra-sensitive, cheap, and widely available) rapid testing...

We present a low-voltage 4-terminal graphene nanoribbon (GNR) device for the detection and measurement of low concentration analytes. The designed device uses a low-bandgap, near-metallic channel whose electronic transport properties aim to resemble the characteristics of commercially-available, large-area graphene devices. The device is demonstrat...

The effects of nanoparticle size on the “macroscopic” mechanical response and interfacial interaction in the case of model nano-reinforced polymers were investigated using molecular dynamics simulations. Different ensembles, of homogeneous polymer matrices, amorphous silica particle, and their binary mixtures were prepared. The binary mixture was m...

We developed a new coarse-grained (CG) molecular dynamics force field for polyacrylamide (PAM) polymer based on fitting to the quantum mechanics (QM) equation of state (EOS). In this method, all nonbond interactions between representative beads are parameterized using a series of QM-EOS, which significantly improves the accuracy in comparison to co...

The atomic-scale fragmentation processes involved in molecules undergoing hypervelocity impacts (HVIs; defined as >3 km/s) are challenging to investigate via experiments and still not well understood. This is particularly relevant for the consistency of biosignals from small-molecular-weight neutral organic molecules obtained during solar system ro...

Nanocomposite generators convert mechanical energy into electrical energy and are attractive low-power solutions for self-powered sensors and wearables. Homogeneous dispersion, high concentration, and orientation of the embedded filler strategies have been assumed to maximize the voltage output in nanocomposite generators. This work contrast these...

https://agu.confex.com/agu/fm20/meetingapp.cgi/Paper/673720

Leaf nitrogen (N) directly correlates to chlorophyll production, affecting crop growth and yield. Farmers use soil plant analysis development (SPAD) devices to calculate the amount of chlorophyll present in plants. However, monitoring large-scale crops using SPAD is prohibitively time-consuming and demanding. This paper presents an unmanned aerial...

Traditional methods to measure spatio-temporal variations in biomass rely on a labor-intensive destructive sampling of the crop. In this paper, we present a high-throughput phenotyping approach for the estimation of Above-Ground Biomass Dynamics (AGBD) using an unmanned aerial system. Multispectral imagery was acquired and processed by using the pr...

Traditional methods to measure spatio-temporal variations in biomass rely on a labor-intensive destructive sampling of the crop. In this paper, we present a high-throughput phenotyping approach for the estimation of Above-Ground Biomass Dynamics (AGBD) using an unmanned aerial system. Multispectral imagery was acquired and processed by using the pr...

The potential for phosphorene-based devices has been compromised by the material's fast degradation under ambient conditions. Its tendency to fully oxidize under O2-rich and humid environments, leads to the loss of its appealing semiconducting properties. However, partially-oxidized phosphorene (po-phosphorene), has been demonstrated to remain stab...

With the increasing power of computation systems, theoretical calculations provide a means for quick determination of material properties, laying out a research plan, and lowering material development costs. One of the most common is Density Functional Theory (DFT), which allows us to simulate the structure of chemical molecules or crystals and the...

The development of new techniques or instruments for detecting and accurately measuring biomarker concentrations in living organisms is essential for early diagnosis of diseases, and for tracking the effectiveness of treatments. In chronic diseases, such as asthma, precise phenotyping can help predict the response of patients to treatments and redu...

Label-free sensors capable of detecting low concentrations of significant biomolecular substances without inducing immune response, would simplify experiments, minimize errors, improve real-time observations, and reduce costs in probing living organisms. This paper presents a first-principles, in-silico derived, all-armchair graphene nanoribbon (ac...

Many material device applications would benefit from thin diamond coatings, but current growth techniques, such as chemical vapor deposition (CVD) or atomic layer deposition require high substrate and gas‐phase temperatures that would destroy the device being coated. The development of freestanding, thin boron‐doped diamond nanosheets grown on tant...

This issue of PNAS features "nonequilibrium transport and mixing across interfaces," with several papers describing the nonequilibrium coupling of transport at interfaces, including mesoscopic and macroscopic dynamics in fluids, plasma, and other materials over scales from microscale to celestial. Most such descriptions describe the materials in te...

The development of new energetic materials (EMs) with improved detonation performance but low sensitivity and environmental impact is of considerable importance for applications in civilian and military fields. Often new designs are difficult to synthesize so predictions of performance in advance is most valuable. Examples include MTO (2,4,6-triami...

According to the World Health Organization (WHO), almost 2 billion people each year are infected worldwide with flu-like pathogens including influenza. This is a contagious disease caused by viruses belonging to the family Orthomyxoviridae. Employee absenteeism caused by flu infection costs hundreds of millions of dollars every year. To successfull...

We use reactive molecular dynamics (RMD) simulations to study the interface between cyclotrimethylene trinitramine (RDX) and Aluminum (Al) with different oxide layers to elucidate the effect of nano-sized Al on thermal decomposition of RDX. A published ReaxFF force field for C/H/N/O elements was retrained to incorporate Al interactions, and then us...

Understanding the structural, thermal, and mechanical properties of thaumasite is of great interest to the cement industry, mainly because it is the phase responsible for the aging and deterioration of civil infrastructures made of cementitious materials attacked by external sources of sulfate. Despite its importance, the effects of temperature and...

The Gaussian Hartree approximated QM (GHA-QM) is the kernel of a new non-adiabatic quantum electron dynamics formulation concept, i.e., evaluating QM energies of the total electronic wavefunction in a force field manner, by the sum of pairwise (3 or 4-body interactions) interactions. This new scheme enables fast computation of QM energies and force...

A detector apparatus includes a field-effect transistor configured to undergo a change in amplitude of a source-to-drain current when at least a portion of charge-tagged molecule translocated through a nano pore. In some implementations, the field-effect transistor is a carbon nanotube field effect transistor and the nano pore is located in a membr...

Presented herein is the progress on developing a new mass analyzer for analysis of the exospheres of planets, moons, and primitive bodies, such as found at Europa or Enceladus. Europa, one of Jupiter's four Galilean moons, may have a subsurface ocean plausibly containing the key ingredients for life as well as sources of chemical energy. Clues to t...

Recently Debe et al. reported that Pt3Ni7 leads to extraordinary Oxygen Reduction Reaction (ORR) activity. However, several reports show that hardly any Ni remains in the layers of the catalysts close to the surface (“Pt-skin effect”). This paradox that Ni is essential to the high catalytic activity with the peak ORR activity at Pt3Ni7 while little...

Modeling non-adiabatic phenomena and materials at extremes has been a long-standing challenge for computational chemistry and materials science, particularly for systems that undergo irreversible phase transformations due to significant electronic excitations. Ab ini- tio and existing quantum mechanics approximations to the Schrödinger equation hav...

By driving molecules electrophoretically through a nano pore, single molecule detection can be achieved. To enhance translocation control, functionalized and non-functionalized electrodes are strategically placed around or above a nano pore. Changes in transmission spectra and input voltage detected by electrodes allow accurate identification of si...

Gallium Nitride (GaN) is a wide bandgap semiconductor with many important applications in optoelectronics, photonics, and high power and high temperature operation devices. Understanding the surface deposition mechanisms and energetics for different precursors is essential to improving thin film crystalline quality and growth process requirements f...

Conventional methods require elevated temperatures in order to dissociate high-energy nitrogen bonds in precursor molecules such as ammonia or hydrazine used for nitride film growth. We report enhanced photodissociation of surface-absorbed hydrazine (N2H4) molecules at low temperature by using ultraviolet surface plasmons to concentrate the excitin...

Introduction: Understanding the physics and chem-istry of hypervelocity collisions of small impactors on spacescrafts and their instruments is critical to their sur-vival and operational accuracy. Unfortunately, high impact energies from small particles (e.g. organic spe-cies or cosmic dust) lead to untraceable adiabatic and non-adiabatic chemical...

This entry reviews the literature on the creation of nanometer-scale spatial positioners, from a kinematic and dynamic standpoint, as one of the basic building blocks for an atomic-scale manipulator (to arrange differently functionalized molecular building blocks into a lattice or any other nanometer-scale object in a specified and complex pattern,...

We develop here the methodology for dramatically accelerating the ReaxFF reactive force field based reactive molecular dynamics (RMD) simulations through use of the bond boost concept (BB), which we validate here for describing hy-drogen combustion. The bond order, under-coordination, and over-coordination concepts of ReaxFF ensure that the BB corr...

First-principles-based force fields prepared from large quantum mechanical data sets are now the norm in predictive molecular dynamics simulations for complex chemical processes, as opposed to force fields fitted solely from phenomenological data. In principle, the former allow improved accuracy and transferability over a wider range of molecular c...

We use first-principles quantum mechanical calculations to study diamond thin film growth on the (100) surface using CCl radicals as the carbon source. Our results show that CCl inserts into the surface dimer C–C bonds with a barrier of 10.5 kcal/mol, roughly half of the energy required for traditional CH2 insertion (22.0 kcal/mol). In addition to...

We report reactive molecular dynamics simulations using the ReaxFF reactive force field to examine shock-induced hot-spot formation followed by detonation initiation in realistic (2.7 million atoms) models of polymer bonded explosives (PBX) with nonplanar interfaces. We considered here two energetic materials (EMs) pentaerythritol tetranitrate (PET...

We describe the application of the ReaxFF reactive force field with short-range distance-dependent exponential inner wall corrections and the non-adiabatic electron Force Field (eFF) for studying the hypervelocity impact (HVI) effects on material properties. In particular, to understanding nonequilibrium energy/mass transfer, high strain/heat rate...

The NASA/ESA Cassini probe of Saturn analyzed the molecular composition of plumes emanating from one of its moons, Enceladus, and the upper atmosphere of another, Titan. However, interpretation of this data is complicated by the hypervelocity (HV) flybys of up to ∼18  km/sec that cause substantial molecular fragmentation. To interpret this data we...

Metallic glasses have been established to have unique properties such as ductility, toughness, and soft magnetism with promising engineering applications. However, the glass-forming ability (GFA) has not been sufficient to synthesize the bulk metallic glasses (BMGs) required for many engineering applications. Attempts to develop the understanding o...

Using force fields trained using the new quantum mechanics (QM) methods (XYGJ-OS and PBE-ulg), we have developed new strategies to predict equil. conformations of macromol. systems.We have also developed new methods to ext. the thermodn. properties (entropies and free energies) for individual parts of heterogeneous composites and to follow these ch...

This chapter outlines our progress toward developing a first-principles-based hierarchical multiscale, multiparadigm modeling and simulation framework for the characterization and optimization of electronic and chemical properties of nanoscale materials and devices. In our approach, we build from the bottom-up by solving the quantum-mechanical (QM)...

Ettringite is a hexacalcium aluminate trisulfate hydrate mineral that forms during Portland cement hydration. Its presence plays an important role in controlling the setting rate of the highly reactive aluminate phases in cement paste and has also been associated with severe cracking in cured hardened cement. To understand how it forms and how its...

Electron force field (eFF) wave-packet molecular-dynamics simulations of the single shock Hugoniot are reported for a crystalline polyethylene (PE) model. The eFF results are in good agreement with previous density-functional theories and experimental data, which are available up to 80 GPa. We predict shock Hugoniots for PE up to 350 GPa. In additi...

First-principles quantum mechanics methods are inadequate for accurately describing the effects of thermal, mechanical, chemical or radiation excitations that may occur in materials operating under extreme conditions, or impractical to use due to the prohibitive scaling cost of propagating the total Schrodinger equation for a large set of atoms. In...

It has long been observed that brittle fracture of materials can lead to emission of high energy electrons and UV photons, but an atomistic description of the origin of such processes has lacked. We report here on simulations using a first-principles-based electron force field methodology with effective core potentials to describe the nonadiabatic...

The fundamental processes in shock-induced instabilities of materials remain obscure, particularly for detonation of energetic materials. We simulated these processes at the atomic scale on a realistic model of a polymer-bonded explosive (3,695,375 atoms/cell) and observed that a hot spot forms at the nonuniform interface, arising from shear relaxa...

We have used the recently developed electron force field (eFF) and ReaxFF reactive force field to simulate the hypervelocity impacts experienced by the Cassini ion and neutral mass spectrometer during the Enceladus and Titian encounters.

We describe the first principle-based electron force field (eFF) methodology for modeling the simultaneous dynamics of electrons and nuclei (eMD) evolving nonadiabatically under transient extreme conditions. We introduce the parallel implementation of eFF (pEFF) that makes it practical to perform simulations of the nonadiabatic dynamics of material...

We expect that systematic and seamless computational upscaling and downscaling for modeling, predicting, or optimizing material and system properties and behavior with atomistic resolution will eventually be sufficiently accurate and practical that it will transform the mode of development in the materials, chemical, catalysis, and Pharma industrie...

Invited on behalf of the US Army Research Laboratory (ARL), to give a short briefing at the Multi-Scale Multi-Disciplinary Modeling (MMM) of Electronic Materials workshop held at the Fairfax Marriot at Fair Oaks, Fairfax, Virginia from Wednesday, September 1, 2010 to Thursday, September 2, 2010. The workshop was part of ARL’s process in developing...

Atomistic-level molecular dynamics (MD) is used to investigate the thermodynamical and mechanical properties of candidate polymer-based hydrogel networks for tissue scaffold-support therapies that serve a predominantly biomechanical function, in particular articular cartilage. The MD uses force field parameters based on quantum mechanical calculati...

This paper describes the design and development of the modeling and simulation environment for the robotic manipulators named ROBOMOSP (Robotics Modeling and Simulation Platform), which addresses important limitations of existing software for this purpose, under a highly parametric interface ideal for academics and research. The ROBOMOSP software p...

Modelar y simular tridimensionalmente sistemas robóticos manipuladores es importante debido al alto costo de inversión requerido en la implantación de los mismos en una aplicación real. El presente articulo describe las principales partes que conforman el sistema modular de software incorporados en ROBOMOSP [1], una plataforma que se constituye en...

Final undergraduate project written and defended by the authors in order to earn a bachelor's degree in Computer Science and Software Engineering given by the Pontificia Universidad Javeriana - Cali Campus. The objective of this research project was to develop the graphical user interface, the 3D motor engine, and the software architecture of the R...

A novel algorithm for the solution of the inverse dynamics problem is presented and augmented to the solution of the equations of motion (EOM) for rigid multibody chains using explicit constraint components of force. The unified model corresponds to an optimal, strictly parallel, time, space, and processor lower bound solution to the dynamics of ac...

Over the past two years at the Materials and Process Simulation Center, we have been developing simulation approaches for studying the molecular nanomachine designs pioneered by Drexler and Merkle. These nanomachine designs, such as planetary gears and neon pump, are described with atomistic details and involve up to 10 000 atoms. With the Dreidin...

In this paper, a novel algorithm for solution of the constrained equations of motion with application to simulation of the molecular dynamics systems is presented. The algorithm enables the solution of equations of motion with an internal coordinates model wherein the high-frequency oscillations are frozen by explicit inclusion of hard constraints...

In this paper a novel algorithm for solution of constrained equations of motion with application to simulation of molecular dynamics systems is presented. The algorithm enables the solution of equation of motion with an internal coordinates model wherein the high frequency oscillations are freezed by explicit inclusion of hard constraints in the sy...