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1

Mainstream and evolutionary views of technology, economic growth and catching up

Perilla Jimenez, Juan Ricardo

Journal:

Journal of Evolutionary Economics

Year:

2019

Language:

english

File:

PDF, 749 KB

english, 2019

2

Molecular Dynamics Simulations of an Entire HIV Virion

Reddy, Tyler, Perilla, Juan R.

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 44 KB

english, 2019

3

Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC

Wright, Eric, Ferrato, Mauricio, Bryer, Alexander J., Searles, Robert, Perilla, Juan R., Chandrasekaran, Sunita, Schneidman-Duhovny, Dina

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 4.36 MB

2020

4

Computing ensembles of transitions from stable states: Dynamic importance sampling

Juan R. Perilla, Oliver Beckstein, Elizabeth J. Denning, Thomas B. Woolf

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 2.19 MB

english, 2011

5

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions

Oliver Beckstein, Elizabeth J. Denning, Juan R. Perilla, Thomas B. Woolf

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 1.38 MB

english, 2009

6

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

Zhao, Gongpu, Perilla, Juan R., Yufenyuy, Ernest L., Meng, Xin, Chen, Bo, Ning, Jiying, Ahn, Jinwoo, Gronenborn, Angela M., Schulten, Klaus, Aiken, Christopher, Zhang, Peijun

Journal:

Year:

2013

Language:

english

File:

PDF, 2.10 MB

english, 2013

7

[IEEE 2010 IEEE ANDESCON - Bogota, Colombia (2010.09.15-2010.09.17)] 2010 IEEE ANDESCON - Small scale prototype of a DC/DC multilevel converter for high voltage applications

Castano, Juan Alejandro, Perilla, Gabriel, Diez, Rafael, Patino, Diego

Year:

2010

Language:

english

File:

PDF, 1.34 MB

english, 2010

8

Dynamic Importance Sampling Calculations on ECD Epitelial Growth Factor Receptor Conformational Changes

Perilla, Juan R., Leahy, Dan, Woolf, Thomas B.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 59 KB

english, 2011

9

Computing Transitions in Macromolecular Systems: Dynamic Importance Sampling

Perilla, Juan R., Nagarajan, Anu, Beckstein, Oliver, Woolf, Thomas B.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 35 KB

english, 2009

10

Understanding the conformational changes in Ca-APTase using Coarse-grained and All-atom simulations with Dynamic Importance Sampling

Nagarajan, Anu, Perilla, Juan R., Woolf, Thomas B.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 37 KB

english, 2009

11

Towards Finding a Better Reaction Coordinate: NtrC and DIMS

Perilla, Juan R., Woolf, Thomas B.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 36 KB

english, 2011

12

Towards the prediction of order parameters from molecular dynamics simulations in proteins

Perilla, Juan R., Woolf, Thomas B.

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 1.25 MB

english, 2012

13

Molecular dynamics simulations of transitions for ECD epidermal growth factor receptors show key differences between human and drosophila forms of the receptors

Perilla, Juan R., Leahy, Daniel J., Woolf, Thomas B.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 3.18 MB

english, 2013

14

Molecular dynamics simulations of large macromolecular complexes

Perilla, Juan R, Goh, Boon Chong, Cassidy, C Keith, Liu, Bo, Bernardi, Rafael C, Rudack, Till, Yu, Hang, Wu, Zhe, Schulten, Klaus

Journal:

Current Opinion in Structural Biology

Year:

2015

Language:

english

File:

PDF, 2.33 MB

english, 2015

15

Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis

Goh, Boon Chong, Perilla, Juan R., England, Matthew R., Heyrana, Katrina J., Craven, Rebecca C., Schulten, Klaus

Journal:

Year:

2015

Language:

english

File:

PDF, 4.36 MB

english, 2015

16

Atomistic Characterization of the HIV Capsid from Molecular Dynamics Simulations

Perilla, Juan R., Schulten, Klaus

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 42 KB

english, 2015

17

Dynamic allostery governs cyclophilin A–HIV capsid interplay

Lu, Manman, Hou, Guangjin, Zhang, Huilan, Suiter, Christopher L., Ahn, Jinwoo, Byeon, In-Ja L., Perilla, Juan R., Langmead, Christopher J., Hung, Ivan, Gor'kov, Peter L., Gan, Zhehong, Brey, William,

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.89 MB

english, 2015

18

Contributions of charged residues in structurally dynamic capsid surface loops to Rous sarcoma virus assembly

Heyrana, Katrina J., Goh, Boon Chong, Perilla, Juan R., Nguyen, Tam-Linh N., England, Matthew R., Bewley, Maria C., Schulten, Klaus, Craven, Rebecca C.

Journal:

Journal of Virology

Year:

2016

Language:

english

File:

PDF, 1.64 MB

english, 2016

19

All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

Perilla, Juan Roberto, Hadden, Jodi Ann, Goh, Boon Chong, Mayne, Christopher G., Schulten, Klaus

Journal:

The Journal of Physical Chemistry Letters

Year:

2016

Language:

english

File:

PDF, 6.14 MB

english, 2016

20

Elucidating the Structure, Dynamics and Functions of an Immature Retrovirus in Atomistic Detail

Goh, Boon Chong, Perilla, Juan R., Heyrana, Katrina J., England, Matthew R., Craven, Rebecca C., Schulten, Klaus

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 39 KB

english, 2016

21

Cyclophilin a Stabilizes the Mature HIV-1 Capsid through a Novel Non-Canonical Binding Site

Zhang, Peijun, Liu, Chuang, Perilla, Juan R., Byeon, In-Ja, Ning, Jiying, Ahn, Jinwoo, Aiken, Chris, Gronenborn, Angela M., Polenova, Tatyana, Schulten, Klaus

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 46 KB

english, 2015

22

Cryo-Electron Tomography and Computer Simulations Reveal Distinct CheA Kinase Conformation in Bacterial Chemotaxis Signaling Receptor Complex

Himes, Benjamin A., Cassidy, C. Keith, Ma, Jun, Alvarez, Frances Joan D., Perilla, Juan R., Zhao, Gongpu, Schulten, Klaus, Zhang, Peijun

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 44 KB

english, 2015

23

Molecular Insights into the Signaling Mechanism of the Histidine Kinase CheA within an Intact Bacterial Chemosensory Array

Cassidy, C. Keith, Himes, Benjamin, Alvarez, Frances Joan D., Perilla, Juan R., Ma, Jun, Zhao, Gongpu, Zhang, Peijun, Schulten, Klaus

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 40 KB

english, 2015

24

EXPORTACIONES Y POLÍTICAS COMERCIALES ÓPTIMAS PARA LA INDUSTRIA TEXTIL Y DE CONFECCIONES: Casos de Colombia y México, 1990-2002

Fernando Mesa and Juan Ricardo Perilla

Journal:

El Trimestre Económico

Year:

2007

File:

PDF, 2.26 MB

2007

25

HIV-1 Capsid Function is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD

Zhang, Huilan, Hou, Guangjin, Lu, Manman, Ahn, Jinwoo, Byeon, In-Ja L, Langmead, Christopher J., Perilla, Juan R., Hung, Ivan, Gor'kov, Peter L., Gan, Zhehong, Brey, William W., Case, David A., Schult

Journal:

Journal of the American Chemical Society

Year:

2016

Language:

english

File:

PDF, 2.61 MB

english, 2016

26

CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

Perilla, Juan R., Zhao, Gongpu, Lu, Manman, Ning, Jiying, Hou, Guangjin, Byeon, In-Ja L., Gronenborn, Angela M., Polenova, Tatyana, Zhang, Peijun

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 4.53 MB

english, 2017

27

Cryoem Structure of the Full Length Dynamin-Like MxB at 4.6 Å Resolution

Alvarez, Frances Joan D., He, Shaoda, Perilla, Juan R., Jang, Sooin, Prevelige, Peter E., Engelman, Alan, Schulten, Klaus, Scheres, Sjors, Zhang, Peijun

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 47 KB

english, 2017

28

Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site

Liu, Chuang, Perilla, Juan R., Ning, Jiying, Lu, Manman, Hou, Guangjin, Ramalho, Ruben, Himes, Benjamin A., Zhao, Gongpu, Bedwell, Gregory J., Byeon, In-Ja, Ahn, Jinwoo, Gronenborn, Angela M., Preveli

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 4.26 MB

english, 2016

29

Juvenile Psammomatoid Ossifying Fibroma

Cárdenas-Perilla, Rodrigo, Santamaria, Consuelo, Muñoz-Acosta, Juan Manuel

Journal:

Clinical Nuclear Medicine

Year:

2016

Language:

english

File:

PDF, 200 KB

english, 2016

30

Tachinid Fly (Diptera: Tachinidae) Parasitoids of Danaus plexippus (Lepidoptera: Nymphalidae)

Oberhauser, Karen, Elmquist, Dane, Perilla-López, Juan Manuel, Gebhard, Ilse, Lukens, Laura, Stireman, John

Journal:

Annals of the Entomological Society of America

Year:

2017

Language:

english

File:

PDF, 243 KB

english, 2017

31

[IEEE 2017 IEEE Workshop on Power Electronics and Power Quality Applications (PEPQA) - Bogota, Colombia (2017.5.31-2017.6.2)] 2017 IEEE Workshop on Power Electronics and Power Quality Applications (PEPQA) - Self-balancing control strategy for a battery based H-bridge multilevel inverter

Guavita, Juan, Diez, Rafael, Patino, Diego, Ruiz, Fredy, Perilla, Gabriel

Year:

2017

Language:

english

File:

PDF, 842 KB

english, 2017

32

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

Perilla, Juan R., Schulten, Klaus

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 3.13 MB

english, 2017

33

CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction

Alvarez, Frances J. D., He, Shaoda, Perilla, Juan R., Jang, Sooin, Schulten, Klaus, Engelman, Alan N., Scheres, Sjors H. W., Zhang, Peijun

Journal:

Science Advances

Year:

2017

Language:

english

File:

PDF, 2.16 MB

english, 2017

34

Length of encapsidated cargo impacts stability and structure of in vitro assembled Alphavirus core-like particles

Rayaprolu, Vamseedhar, Moore, Alan, Wang, Joseph Che-Yen, Goh, Boon Chong, Perilla, Juan, Zlotnick, Adam, Mukhopadhyay, Suchetana

Journal:

Journal of Physics Condensed Matter

Year:

2017

Language:

english

File:

PDF, 1.52 MB

english, 2017

35

First Record of Myelobia smerintha (Hübner) (Lepidoptera: Pyralidae: Crambinae) in Sugarcane in Colombia

Sandoval-Cáceres, Yuly P., Vergara-Navarro, Erika V., Landry, Bernard, Perilla-López, Juan M., Barreto-Triana, Nancy

Journal:

Journal of Agricultural and Urban Entomology

Year:

2017

Language:

english

File:

PDF, 552 KB

english, 2017

36

Quenching protein dynamics interferes with HIV capsid maturation

Wang, Mingzhang, Quinn, Caitlin M., Perilla, Juan R., Zhang, Huilan, Shirra, Randall, Hou, Guangjin, Byeon, In-Ja, Suiter, Christopher L., Ablan, Sherimay, Urano, Emiko, Nitz, Theodore J., Aiken, Chri

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 3.64 MB

english, 2017

37

Energetics of Nucleotide Translocation through HIV-1 CA Hexamer

Xu, Chaoyi, Perilla, Juan

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 43 KB

english, 2018

38

Atomic-Level Characterization of the HIV-1 Capsid and Host-Pathogen Interactions from Molecular Dynamics Simulations

Perilla, Juan R.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 41 KB

english, 2018

39

Critical Role of the HTLV-1 Capsid N-Terminal Domain for Gag-Gag Interactions and Virus Particle Assembly

Martin, Jessica L., Mendonça, Luiza, Marusinec, Rachel, Zuczek, Jennifer, Angert, Isaac, Blower, Ruth J., Mueller, Joachim D., Perilla, Juan R., Zhang, Wei, Mansky, Louis M.

Journal:

Journal of Virology

Year:

2018

Language:

english

File:

PDF, 1.25 MB

english, 2018

40

All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits

Hadden, Jodi A, Perilla, Juan R, Schlicksup, Christopher John, Venkatakrishnan, Balasubramanian, Zlotnick, Adam, Schulten, Klaus

Journal:

Year:

2018

Language:

english

File:

PDF, 8.44 MB

english, 2018

41

CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling

Cassidy, C Keith, Himes, Benjamin A, Alvarez, Frances J, Ma, Jun, Zhao, Gongpu, Perilla, Juan R, Schulten, Klaus, Zhang, Peijun

Journal:

Year:

2015

Language:

english

File:

PDF, 3.83 MB

english, 2015

42

Inositol phosphates are assembly co-factors for HIV-1

Dick, Robert A., Zadrozny, Kaneil K., Xu, Chaoyi, Schur, Florian K. M., Lyddon, Terri D., Ricana, Clifton L., Wagner, Jonathan M., Perilla, Juan R., Ganser-Pornillos, Barbie K., Johnson, Marc C., Porn

Journal:

Year:

2018

Language:

english

File:

PDF, 18.01 MB

english, 2018

43

Author Correction: Inositol phosphates are assembly co-factors for HIV-1

Dick, Robert A., Zadrozny, Kaneil K., Xu, Chaoyi, Schur, Florian K. M., Lyddon, Terri D., Ricana, Clifton L., Wagner, Jonathan M., Perilla, Juan R., Ganser-Pornillos, Barbie K., Johnson, Marc C., Porn

Journal:

Year:

2018

File:

PDF, 331 KB

2018

44

All-atom virus simulations

Hadden, Jodi A, Perilla, Juan R

Journal:

Current Opinion in Virology

Year:

2018

Language:

english

File:

PDF, 1.02 MB

english, 2018

45

Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations

Quinn, Caitlin M., Wang, Mingzhang, Fritz, Matthew P., Runge, Brent, Ahn, Jinwoo, Xu, Chaoyi, Perilla, Juan R., Gronenborn, Angela M., Polenova, Tatyana

Journal:

Proceedings of the National Academy of Sciences

Year:

2018

Language:

english

File:

PDF, 1.62 MB

english, 2018

46

Comparison of four methods for quantitative assessment of 99mTc-MDP SPECT in patients with suspected condylar hyperplasia

López Buitrago, Diego F., Muñoz Acosta, Juan M., Cárdenas-Perilla, Rodrigo A.

Journal:

Revista Española de Medicina Nuclear e Imagen Molecular (English Edition)

Year:

2018

File:

PDF, 1.15 MB

2018

47

Aprostocetus chilophagae new species (Hymenoptera: Eulophidae) from South Dakota, with taxonomic notes on A. bromi (Kostjukov) and A. nebraskensis (Girault)

JOHNSON, PAUL J., YEFREMOVA, ZOYA A., MANUEL, JUAN, LÓPEZ, PERILLA, YEGORENKOVA, EKATERINA N.

Journal:

Year:

2018

Language:

english

File:

PDF, 4.13 MB

english, 2018

48

Understanding Protein HD Exchange Data using Molecular Dynamics Simulations

Sanap, Dipak B., Hemanth Giri Rao, V.V., Perilla, Juan R., Gosavi, Shachi

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 42 KB

2019

49

Understanding Protein HD Exchange Data using Molecular Dynamics Simulations

Sanap, Dipak B., Hemanth Giri Rao, V.V., Perilla, Juan R., Gosavi, Shachi

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 42 KB

english, 2019

50

Mainstream and evolutionary views of technology, economic growth and catching up

Perilla Jimenez, Juan Ricardo

Journal:

Journal of Evolutionary Economics

Year:

2019

File:

PDF, 749 KB

2019

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